Ross walked with one out off Nieve (1-2) and took third on a single by Ronny Paulino. Nieve's first pitch to pinch-hitter Dan Uggla was a breaking ball in the dirt that bounced away from catcher Rod Barajas, and Ross slid across home plate with the winning run.
Johan Santana and Josh Johnson each went seven innings and left with the score 1-all.
Leo Nunez (2-0) pitched a scoreless ninth after Luis Castillo reached second on a single and an error to start the inning. David Wright struck out for the 46th time this year to end the threat.
Each of New York's past 10 games have been decided by less than three runs. The Mets, starting a three-city, eight-game trip, have the fewest road wins in the majors and are now 4-9 away from home.
The Marlins won despite continuing to struggle offensively. They've scored 28 runs in their past nine games.
Gaby Sanchez went 3 for 3 against Santana, but the Marlins went 1 for 5 with runners in scoring position and grounded into three double plays.
Santana's pinpoint location betrayed him only once — on a throw to second base. His misfire led to an unearned run in the third. He gave up six hits and struck out five.
Johnson allowed only three hits, all singles in the span of five batters in the second inning, including a two-out hit by Rod Barajas. Johnson struck out seven and walked none.
The Marlins are last in the majors in fielding, but defense kept them in the game. Angel Pagan was twice robbed of a hit when left fielder Chris Coghlan and second baseman Brian Barden made diving plays, and first baseman Sanchez's leaping catch of a liner by Santana with two on ended the second inning.
Florida's opponent scored first for the 12th time in the past 13 games. The Mets scored in the second on singles by Jason Bay, Ike Davis and Barajas.
Florida made it 1-1 with an unearned run in the third. Sanchez singled and advanced when Santana threw high to second after fielding Johnson's bunt. Coghlan followed with a run-scoring single.
NOTES: Before the game, the Marlins recalled C Brett Hayes from Triple-A New Orleans and optioned OF Bryan Petersen to New Orleans. Hayes can also play left field and first base. ... Johnson made a bad throw in the sixth inning for the eighth error by a Marlins pitcher this season. ... Uggla, who is 1 for 19 against Santana with 10 strikeouts, was held out of the starting lineup for the first time this season. ... Mets manager Jerry Manuel on stealing signs: "I try to pick up everything I can. I just don't use binoculars." The Philadelphia Phillies' bullpen coach was caught on camera this week peering through binoculars from the bullpen bench at Coors Field. ... The Marlins are the only team in the majors without a home run by a left-handed hitter.