
Made numerous edits to GamerProfile.xml to attempt to fix the black screen issue with no sucess.
Worked perfectly on lintial install. Played for about three hours with no issues. Returned the next day and the game freezes on a black screen after the inital loading screen. Have tried multiple fixes including reinstalling, switching Proton versions, editing config files and deleting save data. So far no change in behaviour. Will update if I find a fix.

Frame rate cap is set based on V-Sync enabled in-game. Keep this in mind, because it's not always clear.
Game does not support Mixed Input. Mouse & Keyboard layout using Steam Input is one advised way, but keep in mind there are several quick-time events that are mapped to specific keyboard keys. Either adjust and deal with them, or just use a Gamepad binding.
Save data does NOT work with Steam Cloud; it depends on the Ubisoft Launcher running in the background. It may fail for no reason, but keep retrying until the error box no longer shows up. There's no documented reason why it fails repeatedly.
If launched from Steam, game may not start. If game is closed, Steam may think it's still running because a required launcher running in the background either did not launch the game or self-close when the game is exited. On Fedora KDE desktop, the launcher is accessible from taskbar on the bottom-right (by default), so use that with a mouse to manually launch the game or close the launcher.
The launcher also handles syncing Ubisoft's achievements with Steam's.
Multiplayer (both Co-op and Versus) is removed as of 2025
The way played now is a compromise between Ubisoft's obsession with tying even old games' purchase history and save data to launchers, and the accessibility to play as designed for Steam titles. There is a required launcher, but it's not invasive, and it's easily installed properly along with the game automatically with Proton.

Ubisoft Connect can be finnicky, but game started up fine and played from start to end with no crashes, etc.
Ubisoft Save Sync wasn't working at all and it seems like there is no steam cloud for Far Cry 3 or at least didn't work for me.

PROTON_USE_WOW64=1 %command%
The mfc100.dll
is now required, probably by Ubisoft Connect, and is missing. Had to add it with protontricks:
PROTON_USE_WOW64=1 protontricks 220240 mfc100

You just need to adjust some graphical settings to achieve 30-40FPS and it is a very enjoyable experience.
The game runs great, the only real annoyance is the mandatory of the Uplay launcher

Ubisoft Connect/ Uplay is required. It can sometimes have issues, Does not have an offline mode and you have to type your password in each time you launch the game.
When bringing up the map there seems to be a audio issue where the music slow changes to a crackle. It is easily ignored but it is there.
There were some odd bugs with the plants physics.
While the game works out of the box there are some odd bugs here and there with the physics and audio but it isn't game runing.

DXVK_ASYNC=1 DXVK_HDR=0
Blinking issue is usually due to DXVK’s HDR handling not playing nice, setting DXVK_HDR=0 tells DXVK to not try to use HDR.
If HDR is disabled in the OS, the game should run without issues.

Game closing instantly on start-up
Initially, downloaded the game on a fresh system but it would immediately close on start-up.
The issue is that Uplay is not automatically downloaded with the game but is required in order to run it. I was able to fix this by downloading a more 'recent' Ubisoft title in my library (Far Cry 5, for instance) which installs Uplay. Only then does Far Cry 3 work normally.
For any 32:9 users like me, note that this game seems to have serious UI scaling issues and given its age, things will look off. You can enable forced letterbox mode but even then the icons are quite low-res compared to what you might expect.

at first launch didnt prompt anything but after second install worked perfectly
potential cause is meddling with wine, lutris or proton versions
nothing happens after pressing play button

Initial loading screen takes 10 minutes
Works just fine with Proton GE, Variable Refresh Rate works with v-sync 1 frame too and framerate is as stable as on windows!
DXVK_ASYNC=1 gamemoderun %command%

Micro-freezing in fullscreen if v-sync is disabled
Not sure how to not get it to stutter and/or freeze without having to enable v-sync but otherwise it works fine

The game wouldn't install uPlay when I intially tried running it. So it wouldn't launch. I fixed this by installing and running a different ubisoft title (Scott Pilgrim vs. The World in this case) and that installed uPlay. After that I was able to run the game without any issues.

broken after update ;(
After a very recent game update, the game will not launch. No obvious indications of why with PROTON_LOG=1. I did see RPC_S_SERVER_UNAVAILABLE but I'm not sure this is the issue

dont work
PROTON_LOG=1 %command%
Installed Ubisoft Connect manually, disabled Steam & Ubisoft overlay, but it won’t start. mfc100.dll error persists after installing VC++ 2010.

The game works immediately after installation
After installation, the game works immediately, you just need to log in to your Ubisoft account each time you start the game, at least in my case.

game-performance %command%
The Ubisoft launcher will ask for your password every time. The game doesn't seem to inhibit screensaver so during cutscenes my screen would dim or turn off. Added the launch option to force performance mode.
WINE_CPU_TOPOLOGY=29 %command%
I only needed to do: Install ProtonUp-Qt, and within the app GE-Proton9-22 Restart Steam and select GE-Proton in game's properties

Needed to log into Ubisoft Connect every time you launch the game. Very annoying.
The crackling was very minor. Slightly noticeable whilst driving.
I set my Refresh Rate to 45 Hz. Game worked happily. No framerate drops yet.

MANGOHUD=1 MANGOHUD_CONFIG=cpu_temp,gpu_temp,ram,vram gamemoderun DXVK_ASYNC=1 %command%
O game rodou tranquilamente com as alterações que fiz. Por padrão sempre coloco nos games a linha de comando "MANGOHUD=1 MANGOHUD_CONFIG=cpu_temp,gpu_temp,ram,vram gamemoderun DXVK_ASYNC=1 %command%" juntamente com o ProtonGE, e se rodar, não testo outra config. Nesse caso o game está aprovado, e ainda rodou melhor do que no Windows 10, já que o game é mal otimizado para maquinas muito fracas, e máquinas mais recentes tem problemas de compatibilidade ocasionando lentidão, não no caso do Linux... Vai entender! kkk

PULSE_LATENCY_MSEC=90 %command%
Cannot get audio to work properly no matter what runner I use, previous reports stated PULSE_LATENCY_MSEC=90 was able to resolve, but has had no such effect on my game. PULSE_LATENCY_MSEC seems to have no effect on the process at all as raising this value does not cause the audio latency to increase at all. I was able to test in Lutris games and noticed that PULSE_LATENCY_MSEC is respected there in a few games, but not on several steam games including this one.
After some time playing fine the game start to "stutter"
No matter which version of steam-provided proton or ge-proton I try, the game does not start

Game doesn't launch
Game refuses to launch, pressing play nothing really happens other than steam reporting that I'm playing the game for a few seconds.

Works
Performs very well

Had to disable Steam Overlay, otherwise it wouldnt start

Download the UbisoftConnectInstaller ( https://www.ubisoft.com/en-us/ubisoft-connect/download )
Add the installer as a non-steam-game to Steam and execute it (Compatibility mode - Proton 9.0.2 - might also work on newer/older versions)
Remove the installer from your steam-games-list and add the now installed Ubisoft Connect ( UbisoftConnect.exe ) as a non-steam-game to Steam
Open Ubisoft Connect (Compatibility mode - Proton Experimental) and download Far Cry 3
Once the download has finished, open the "Far Cry 3"-directory
Rename the file " FC3Update.exe " to " FC3Update.exe.backup "
Create a shortcut called " FC3Update.exe " that points to the file " farcry3_d3d11.exe "
How to create a shortcut: 7.1.: Right-click in the "Far Cry 3"-directory --> "Create new" (in german: "Neu erstellen") --> "shortcut to file or directory" (in german: "Verknüpfung zu Datei oder Ordner")
Start Ubisoft Connect via Steam
Start Far Cry 3
Disclaimer:
It might also work with other compatibility modes, your mileage may vary.
A really, really big thanks to HazMan07 !
gamemoderun %command%
mangohud gamemoderun %command%

Doesn't run at all. Hit Play and nothing happends
I tried force launching Ubisoft Connect, and after that, the game runs to the main menu but still crashes when trying to start the story.

Had to disable the Steam overlay - otherwise the game just infinitely loads once it opens. There is some minor artifacting but it is not that prevelant.

The game will not launch at all
There was a point where the Ubisoft Connect splash screen would pop up but after that, nothing has worked. I have tried every proton version under the sun and it will just not turn on for me.

If the game gets stuck on the loading screen, try to disable Steam overlay.

Steam Overlay
The game runs perfect, just remember to disable Steam Overlay because for some reason the new overlay is making the game stuck on Loading screen and never go to the menu.

black screen and crash before startup

Disabled Steam overlay for this game.

Switched back to Proton 8.0