It says in the documentation (the last section - "Working with Virtual Environments"):

For Python 3 add the following lines to the top of your .wsgi file:

activate_this = '/path/to/env/bin/activate_this.py'
with open(activate_this) as file_:
    exec(file_.read(), dict(__file__=activate_this))

However activate_this.py is no longer present in pyvenv (see http://bugs.python.org/issue21496), thus the above code doesn't work. I found a stackoverflow answer where it said that just copying activate_this.py from a 2.7 virtualenv might work, however I didn't go down that route.

How I managed to get it working:

I added WSGIPythonHome /path/to/env to the top level of my apache config (ie. outside of VirtualEnv). However that might be a little to big of a hammer if people want to run multiple applications in the same Apache instance. In that case setting python-path on WSGIDaemonProcess might work (however I didn't try it out).