Red Sox center fielder Jacoby Ellsbury was replaced in the second after he jammed his right heel sliding back to first base on a pickoff attempt in the first. He will be re-evaluated Monday.
Shane Victorino, Dustin Pedroia and Mike Napoli hit consecutive singles to start the third. Jimmy Rollins committed an error on a ground ball from Will Middlebrooks, which allowed two runs to score to make it 5-0.
Napoli later scored on a sacrifice fly from Bradley, giving Bradley four RBIs on the day.
Ben Revere drove in Humberto Quintero and later scored as the Phillies cut the deficit to 6-2 in the third. Revere was driven home twice by Chase Utley singles Sunday, the second time cutting the deficit to 6-3 in the fifth.
Utley then homered in the eighth off Red Sox righty Noe Ramirez to make it 6-5. Ryan Howard homered in the Phillies' next at-bat to tie the game.
But Shannon Wilkerson drove in Xander Bogaerts with a ninth-inning single to give Boston the lead for good.
Lee allowed nine hits and six runs (four earned) but was able to strike out seven with no walks in 5 1/3 innings. Red Sox right-hander Brandon Workman allowed three hits, two runs and two walks with one strikeout in three innings.
Up Next: Outfielder Jackie Bradley, who seems to be inching closer to a roster spot, is again scheduled to start for the Red Sox in Monday's 1:05 p.m. ET contest at Sarasota against the Orioles, available on MLB.TV. Minor League right-hander Graham Godfrey will be Boston's starting pitcher. Position players Daniel Nava, Ryan Sweeney, Lyle Overbay and Mike Carp -- who are all battling for roster spots -- will be on the trip.
Todd Zolecki is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.