I faced an issue using Fabric SDK on Android when I reached the 65k method references issue. So, the issue is that both problems need the same solution: override base application class in AndroidMainfest.xml. But you can override it only with one of both - FabricApplication or MultiDexApplication. To make this possible, add this small jar file to your Assets/Plugins/Android directory and in your AndroidManifest.xml file add android:name="io.fabric.unity.android.MultiDexFabricApplication" to your <application> tag.

It simply extends FabricApplication class and add MultiDex.install(this) to the attachBaseContext method. That's how you have both multidex and fabric working together for the majesty of your application!

IMPORTANT! If you have min version of your SDK set to 21 or higher, you don't need to set MultiDexApplication as you main class or call MultiDex.install() anywhere in your app. Therefore you don't need this solution neither, just set a FabricApplication as your main application class.