(Other posts on SO are similar, but none have the specific combination of uwsgi + Flask + virtualenv) (This one is closest)
I installed uwsgi via apt-get. I also tried
I encountered the same and my problem was with the python version where uwsgi was running. uwsgi was running on python2 yet my virtualenv python path was set to python3. This created the conflict, it kept on failing to locate the installed site package.
Double check the python version where uwsgi is running so that it is the same as that set on your virtualenv.