Jacob deGrom pitched six shutout innings and left with a lead, but Miami scored against the Mets' bullpen on a wild pitch and two bases-loaded walks for a 3-all tie going into the ninth.
Brandon Nimmo walked with two outs against Brandon Kintzler (1-2), and Conforto hit his fourth homer to center field, a shot estimated at 425 feet.
''With how great Jake was,'' Conforto said, ''it feels good to get that win tonight.''
''It's a big homer,'' Mets manager Luis Rojas said, ''and one of those wins we haven't haven't had this year - in the ninth to take a lead with two outs, especially after blowing a save.''
DeGrom struck out seven, walked none, allowed four hits and departed after throwing 91 pitches. Working for the first time in 10 days after skipping a turn because of neck stiffness, he touched 100 mph in the first inning and 98 in the sixth.
''Not pitching in 10 days, I was a little rusty, and I got tired quicker than I would have liked,'' deGrom said. ''I was fortunate the bad ones I threw weren't close enough to swing at.''
The Mets' bullpen struggled without right-hander Seth Lugo, who will move into the rotation and start Thursday.
''It's really tough not to have a piece like Lugo in the 'pen,'' Rojas said. ''But we trust our bullpen. They're going to do a good job for us closing games.''
Edwin Diaz (1-0) walked in the tying run in the eighth but pitched a perfect ninth, getting all four of his outs via strikeout.
''Diaz did a good job coming back and showing what he could do,'' Rojas said.
Miami's Pablo Lopez allowed two runs in 6 1/3 innings, raising his ERA to 2.42.
''Great starters' battle,'' Marlins closer Kintzler said. ''It was fun to fun to watch. Great comeback by us. Terrible pitching by me.''
The Marlins have lost five games in a row to fall to 9-9. The Mets improved to 17-7 against Miami over the past two seasons and won at Marlins Park for the fifth time in a row.
New York has outscored Miami 24-10 in the series, with the finale Thursday.
The Marlins trailed 3-1 to start the eighth, but two singles and a walk by Dellin Betances loaded the bases, and he hit Eddy Alvarez to force in a run. Diaz came on and walked Logan Forsythe, batting .138, to tie the score.
Miami scratched out a run in the seventh on a walk, an infield hit, a groundout and a wild pitch.
Wilson Ramos' sacrifice fly for the Mets in the second inning scored the game's first run. They scored again in the seventh on a double by Dominic Smith and Luis Guillorme's RBI single. Smith doubled home a run in the eighth.
Former Olympic speedskating silver medalist Alvarez threw out runners at third base and home plate from his shortstop position for Miami, and won praise from manager Don Mattingly for the heads-up plays.
''I just love the fact that he makes them,'' Mattingly said. ''And he makes them fast. There's no hesitation. It's like that was already preprogrammed. That tells me that he's thinking ahead.''
Alvarez is batting only .206 but has sparkled on defense.
Mets: LHP David Peterson underwent an MRI that showed mild shoulder inflammation but no structural damage. He was scratched Tuesday from his scheduled start and placed on the 10-day injured list.
Mets: Lugo (1-2, 2.61) will make his first start since 2018 on Thursday. He replaces struggling LHP Steven Matz (0-4, 9.00 ERA), who moves to the bullpen.
Marlins: LHP Daniel Castano (0-1, 4.35) is scheduled to start for Miami.
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