Phillies starter Jeremy Hellickson earned the victory after allowing two runs on four hits and a walk in five innings, striking out six.
The Cubs completed their own sweep in Baltimore on Sunday, so the Brewers' lead in the National League Central shrunk to 4 1/2 games.
It was not the way new Milwaukee reliever Tyler Webb wanted to begin his Brewers career. Maikel Franco, Andrew Knapp and Tommy Joseph started the decisive sixth with successive singles against right-hander Rob Scahill before Brewers manager Craig Counsell called for Webb, a left-hander acquired in a trade with the Yankees on Wednesday.