Matt Lindstrom escaped a bases-loaded jam in the ninth by getting pinch-hitter Omir Santos on a game-ending popup. In a curious move by Mets manager Jerry Manuel, the inexperienced Santos batted for fellow catcher and right-handed hitter Ramon Castro, who had two hits and an RBI.
Josh Johnson went toe to toe with Santana for the second time in 17 days and left trailing 3-2 after serving up Fernando Tatis' tiebreaking homer in the sixth, which was upheld after a replay review.
Putz (1-2) entered in the eighth and walked his first two batters before Ronny Paulino's sacrifice advanced both runners.
Ross then lined a single up the middle, sending Florida (13-8) to its second consecutive victory following a seven-game skid.
The Marlins took two of three from New York for the second time this season and improved to 13-5 against the NL East.
The Mets fell to 6-6 at their spacious new ballpark, where they have 10 triples and seven homers. They begin a three-game series Friday in Philadelphia, their first matchup this year with the rival Phillies, who won the 2008 World Series.
Renyel Pinto (1-0) worked a scoreless inning for the win. Lindstrom, a hard-throwing former Mets prospect, got three outs for his fifth save and second in two days.
A dreadful Mets bullpen cost Santana seven potential wins last season - including five meltdowns that came in the ninth inning. The team thought it solved that problem in the offseason by signing record-setting closer Francisco Rodriguez and trading for Putz, but that wasn't the case Wednesday.
Santana and Johnson hooked up for an entertaining duel April 12 in Miami, with Johnson tossing a five-hitter in a 2-1 victory that zipped by in 2 hours, 4 minutes.
Santana struck out 13 over seven innings of three-hit ball in that game, but left fielder Daniel Murphy dropped a fly ball for an error that led to both unearned runs for Florida. That was Santana's only loss in his past 22 starts dating to June 28.
This time, the two-time Cy Young Award winner got off to a shaky start. Cameron Maybin tripled with one out in the first and scored on Wes Helms' sacrifice fly. Cantu followed with his sixth homer - he connected twice and knocked in five runs during Tuesday night's 7-4 victory.
Jose Reyes hit a leadoff triple in the bottom half, though replays showed he might have been out at third. Alex Cora drove in the run with a sacrifice bunt.
Castro tied it 2-all with an RBI single in the fourth after Tatis singled and stole second.
Notes: All-Star SS Hanley Ramirez sat out again because of a sore right hand, but Gonzalez hopes he can play Thursday night at Chicago. Ramirez left Monday night's game after he was hit by John Maine's pitch, and X-rays were negative. ... All-Star 2B Dan Uggla was rested. He is 1 for 17 (.059) with 10 strikeouts against Santana. ... The Marlins traded reliever Logan Kensing to Washington for minor league RHP Kyle Gunderson. Kensing had been designated for assignment Sunday. Gunderson will be assigned to Class-A Jupiter. ... Mets 1B Carlos Delgado (hip) and 2B Luis Castillo (back spasm) sat out again. Manuel thinks both should be ready to play Friday.
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