Uggla's double put Florida in front 4-1 with two outs in the top of the eighth.
Chris Coghlan led Florida with two hits and one RBI.
Jorge Cantu added a hit and a sacrifice fly for the Marlins, who have won the first two contests in the regular season-ending three-game series.
Winner Anibal Sanchez (4-8) yielded a run and five hits in seven innings.
Closer Leo Nunez earned his 26th save with a scoreless ninth.
Jayson Werth led Philadelphia with two hits -- one an eighth-inning two-run homer.
Ryan Howard hit a solo shot and scored twice for the Phillies, who have lost three in a row.
The losing pitcher was starter Cole Hamels (10-11).
Despite its loss, Philadelphia clinched home field advantage in the NL playoffs.