Ryan Howard hit his major league-leading 41st homer, but Philadelphia, which trailed 9-1, couldn't overcome a terrible outing by Kyle Kendrick (11-9), who allowed seven runs and six hits in 1 1-3 innings.
Marlins starter Chris Volstad left after three innings with a bruised right leg. He was hit by Carlos Ruiz's hard grounder leading off the third.
Reliever Eulogio De La Cruz allowed six runs and five hits in two-plus innings, nearly blowing the eight-run lead. Kevin Gregg (7-8) retired the side in the seventh. Matt Lindstrom, the Marlins' eighth pitcher, got the final out for his second save.
Trailing 10-4, the Phillies rallied in the sixth. Howard doubled, Pat Burrell walked and Shane Victorino singled to cut it to 10-5 and chase De La Cruz.
Doug Waechter entered to face Greg Dobbs, who lined a two-run double. Pinch-hitter Matt Stairs followed with an RBI single to make it 10-8. After Chris Coste flied to right, Jimmy Rollins singled and stole second to put the tying run in scoring position.
But Jayson Werth flied out to shallow right and Andrew Miller retired Chase Utley on a foul pop.
The Marlins (73-72) snapped a three-game losing streak and moved back over .500.
Since beating Florida on Aug. 6, Kendrick is 1-4 with an 11.35 ERA in six starts.
Kendrick was skipped in the rotation his last start, allowing ace Cole Hamels to pitch against the Mets on Sunday night. Hamels struggled and the Phillies lost 6-3. Kendrick is likely headed for mop-up duty the rest of the season.
Dan Uggla lined a two-run single and Josh Willingham's sacrifice fly gave Florida a 3-0 lead in the first.
Kendrick couldn't get out of the second. Volstad and Hanley Ramirez hit consecutive one-out doubles. After John Baker walked, Cantu hit a three-run homer to put the Marlins ahead 7-1.
Jacobs connected off J.A. Happ in the fourth to make it 9-1. Jacobs' 32nd homer landed in the Phillies' bullpen in right-center.
Howard hit a two-run drive off De La Cruz in the fourth. Burrell followed with a standup triple, a rarity for the slow-footed slugger, and he scored on Victorino's groundout.
Ross hit a solo shot off Happ leading off the fifth, extending the lead to 10-4.
Notes: Werth had two of Philadelphia's four steals. He's 16-for-17 this season. The Phillies are 121-for-143, the best percentage (84.6) in the majors. ... Since Happ was used, 45-year-old Jamie Moyer likely will start on three days' rest Thursday night against Milwaukee. Happ was being considered for that start. ... Jacobs is one homer shy of tying Carlos Delgado for the club record by a left-handed hitter. Delgado hit 33 in 2005.