Running django migrations on multiple databases simultaneously
If we update the application code, when we push to the master branch,
  all installations detect this, pull the latest version of the code and
  restart the application.

I assume that you have some sort of automation to pull the codes and restart the web server. You can just add the migration to this automation process. Each of the server's settings.py would read the database details from the external file and run the migration for you. 
So the flow should be something like: 

Pull the codes
Migrate 
Collect Static
Restart the web server
We are developing a b2b application with django. For each client, we launch a new virtual server machine and a database. So each client has a separate installation of our application. (We do so because by the nature of our application, one client may require high use of resources at certain times, and we do not want one client's state to affect the others)
Each of these installations are binded to a central repository. If we update the application code, when we push to the master branch, all installations detect this, pull the latest version of the code and restart the application.
If we update the database schema on the other hand, currently, we need to run migrations manually by connecting to each db instance one by one (settings.py file reads the database settings from an external file which is not in the repo, we add this file manually upon installation). 
Can we automate this process? i.e. given a list of databases, is it possible to run migrations on these databases with a single command?