Lee (3-2) broke a personal four-start winless streak, yielding five hits without a walk. The left-hander struck out six in the 102-pitch performance.
Domonic Brown belted a solo homer and Michael Young went 3-for-4 with a two-run double to pace Philadelphia's offense as the Phillies broke a two-game skid.
San Francisco's Madison Bumgarner (3-1) was tagged for five runs on eight hits over six full innings.
Hunter Pence went 3-for-3 with a bases-empty clout as the Giants saw their six-game winning streak snapped.