The Mets left 14 runners on base, stranding at least one in every inning.
The one-run margin was the first this season for the Marlins, the only unbeaten team in the majors. They're 4-0 for the first time in franchise history.
Bonifacio reached on an infield single off Pedro Feliciano (0-1) with one out. Darren O'Day walked Hanley Ramirez, and Cantu singled to left on an 0-1 pitch, with Bonifacio sliding home ahead of the throw.
Bonifacio went 3-for-5, hiking his average to .579. He scored three times and has nine runs this season.
Ramirez and Dan Uggla each hit a solo homer for Florida, and Carlos Beltran hit one for New York.
The Mets scored once in the ninth off closer Matt Lindstrom (1-0) to tie the game. Beltran and Ryan Church singled, and pinch hitter Jeremy Reed hit a two-out RBI single, but pinch hitter Alex Cora grounded out to end the inning.
New York stranded two runners in five of the final six innings.
Bonifacio used his speed to give Florida a 4-3 lead. He reached on a two-out bunt single in the seventh against Bobby Parnell, went to third on a bloop single by John Baker and came home on Ramirez's single.
The loss was the first for the Mets' bullpen after the front office invested heavily in upgrades during the offseason. Parnell and Sean Green each gave up one run.
Mets starter John Maine allowed homers to two of the first five batters he faced, and those were the only hits he gave up before leaving for a pinch hitter after five innings.
Florida starter Anibal Sanchez threw 93 pitches in five scoreless innings, and five relievers followed. Sanchez allowed four hits and three walks but worked out of two jams, helping Marlins starters lower their ERA to 2.38.
Ramirez homered with two out in the first, and Uggla homered leading off the second. The Marlins scored their other run in the sixth when Bonifacio singled, advanced on a balk, took third on an infield hit by Ramirez and came home on Cantu's single.
The Mets managed only one hit - a leadoff single - in the seventh but still rallied from a 3-1 deficit to tie the game. The inning included two walks, a hit batsman, an RBI groundout by Beltran and a sacrifice fly by pinch hitter Fernando Tatis.
Notes: Cantu was back in the lineup after being hit on the left hand by a pitch Wednesday. "A bone had to be sticking out of his hand for him not to be in the lineup," manager Fredi Gonzalez said. ... Marlins RF Cody Ross went 0-for-3 and is batting .067 (1-for-15). ... Of the 499 homers hit by Mets OF Gary Sheffield, more have come at Dolphin Stadium (68) than at any other ballpark... The last time Sanchez faced the Mets was May 2, 2007, his final start before undergoing shoulder surgery. ... RHP Livan Hernandez, who will start Saturday for New York, is 19-19 with a 3.86 ERA in 51 games in Miami.
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