Buehrle (7-8) yielded two runs on seven hits while winning his second straight start for the Marlins. The left-hander issued only one walk and struck out seven.
Mike Dunn tossed a scoreless eighth and Heath Bell collected his 16th save in the ninth as Miami clinched its three-game set against the Phillies.
Stanton socked a solo homer in the first inning and put the Marlins ahead for good with a third-inning RBI single.
Philadelphia's Cole Hamels (10-4) absorbed the loss, surrendering three runs on seven hits in a seven-inning effort.
Hunter Pence went 3-for-4 with a solo homer for the losers.