Rollins drove a 2-2 pitch from Dan Jennings (0-1) into the seats in left. It was the 201st career homer for Rollins, but just the second game ender of his career. The first came June 23, 2010, against Cleveland.
B.J. Rosenberg (1-0) pitched a scoreless 10th for the victory.
Rollins finished with three hits and hot-hitting Chase Utley had two doubles and drove in a run for Philadelphia, which has won 12 of 15 against the Marlins.
Through nine games, Utley is batting .500 with five doubles and eight RBIs.
Tony Gwynn Jr., starting in center and leading off for the second straight day in place of Ben Revere (sore ribs), had a pair of hits.
Stanton finished with three hits and three RBIs for the Marlins. His first homer, measured at 470 feet, cleared the seats in left-center and landed on Ashburn Alley - a popular outfield concessions spot. The fifth-inning solo drive off Jonathan Pettibone pulled Miami to 4-2.
Stanton tied it at 4 in the seventh when he drilled reliever Justin De Fratus' first offering to deep left for a two-run shot. It was the 10th two-homer game for Stanton.
Rollins' RBI single and Utley's run-scoring double gave Philadelphia a 2-0 lead after one.
The Marlins got a run back in the second and would have scored at least two more if not for replay.
Second base umpire Gary Cederstrom called Marcell Ozuna safe at second, saying that Ozuna beat shortstop Rollins to the bag on a forceout after Utley ranged right and threw to Rollins on Stanton's grounder up the middle.
But Phillies manager Ryne Sandberg challenged the call and, after a 2 minute, 27 seconds delay, umpires overturned the call. Replays showed that Rollins touched the bag before Ozuna for the final out.
Adeiny Hechavarria had scored, Christian Yelich likely would have scored and the Marlins then would've had runners on first and second with two outs.
Miami did get some good fortune in the inning as Ryan Howard dropped Rollins' throw to first on Ozuna's grounder to shortstop that would've been the final out. Jarrod Saltalamacchia scored from third on Howard's error.
The Phillies went ahead 4-1 in the third on Utley's double and Howard's single.
Pettibone, activated from Triple-A Lehigh Valley for the game, allowed two runs - one earned - on eight hits in five innings in his season debut. Pettibone is filling in until left-hander Cole Hamels (left biceps tendinitis) returns to the rotation.
Miami starter Nathan Eovaldi went 6 1-3 innings, giving up four runs on seven hits while striking out five and walking none.
NOTES: Hamels pitched six strong innings in a rehab start for Class-A Clearwater on Saturday night, giving up one run on six hits with six strikeouts and no walks. . Revere grounded out pinch-hitting in the 10th. . In order to activate Pettibone, the Phillies sent outright right-hander Brad Lincoln Triple-A Lehigh Valley. . Saturday marked the 10th anniversary of the opening of Citizens Bank Park on April 12, 2004. . Miami's Derek Dietrich was a late scratch from the lineup due to lower back tightness. Jeff Baker started at second for him. . The three-game series concludes at 1:35 Sunday when Philadelphia RHP Kyle Kendrick (0-1, 3.75) faces Marlins RHP Henderson Alvarez (0-2, 4.15).