Thanks to the following GitHub comment for this fix:
Package Control will be uppraded next time package update is triggered, either by automatic updates at ST startup or by manually calling "Package Control: Upgrade All Packages/Overwrite All" via Command Palette.
In case PC3.x is not working, you can
- download https://github.com/wbond/package_control/releases/download/4.0.0-beta2/Package.Control.sublime-package
- call Main Menu > Preferences > Browse Packages...
- navigate to to ../Installed Packages