Lee (6-7) gave up seven hits and a walk but stymied the Mets by striking out 10 en route to a win in his fourth straight start. The left-hander tossed 79 of his 111 pitches for strikes.
Jonathan Papelbon fired a 1-2-3 ninth for his 35th save as Philadelphia took the opener of a three-game series.
Jimmy Rollins and Domonic Brown each socked a solo homer in the victory.
R.A. Dickey (18-6) was tagged with the loss, surrendering three runs (two earned) on five hits in seven frames.
Daniel Murphy knocked in the Mets' only run.