You’ve downloaded the offline installer for the Update. This offline installer will update a previous version of Visual studio 2015 to Update 3. Major Visual Studio versions are installed side-by-side. So your 2013 installation will be left untouched by the 2015 update installer
You’ll need to download the offline installer of “Visual Studio 2015 with Update 3” or first install “Visual Studio 2015 RTM” and then apply the update you’ve downloaded.