While Johnson retired 15 batters in a row, Santana was just as good. The left-hander struck out 13 in seven innings, allowing only three hits. But left fielder Daniel Murphy dropped a two-out fly ball in the second for an error that led to both Florida runs.
Santana (1-1) had made 18 starts in a row without a loss, winning 10 consecutive decisions.
Johnson (2-0) struck out seven, walked one and threw 113 pitches in a fast-paced pitchers' duel that took only 2 hours, 4 minutes.
The 6-foot-7 right-hander was one strike from a three-hit shutout when Carlos Delgado doubled in the ninth. Carlos Beltran followed with an RBI single before Ryan Church's soft liner was caught by left fielder Brett Carroll, who made a backhanded grab at the shoetops.
The Marlins totaled only three hits but ended their season-opening homestand at 5-1, the best start in franchise history. The Mets play their home opener Monday night against San Diego at new Citi Field.
Santana, who departed for a pinch hitter after throwing 98 pitches, walked only one and even managed to keep Emilio Bonifacio off base. Florida's leadoff hitter, who came into the game leading the majors in batting and hits, went 0-for-4 to drop his average to .500.
Santana's 13 strikeouts were his highest total in two seasons with the Mets. He had beaten the Marlins in his five previous starts against them, but this time they made the most of their one big break.
Santana retired his first five batters before he walked Jeremy Hermida on a 3-2 pitch. When Cody Ross lifted a high fly to deep left, Murphy retreated awkwardly to the warning track before the ball deflected off his glove, which allowed Hermida to score.
Ronny Paulino's single on the next pitch brought home Ross for a 2-0 lead.
Jose Reyes was the Mets' lone baserunner until the sixth. He reached on a tapper to the pitcher to start the game when first baseman Wes Helms dropped Johnson's throw for an error, but was thrown out trying to steal.
Luis Castillo ended Johnson's no-hit bid in the sixth with a broken-bat single. Castillo advanced on a sacrifice, but Reyes grounded out to end the threat.
With the score 2-0, David Wright singled with one out in the seventh and Bonifacio bobbled a potential double-play grounder for an error that put the tying run aboard. But Johnson overcame the mistake, turning a comebacker by Beltran into a 1-6-3 double play, then heading for the dugout with a pump of his fist.
The Mets put runners at the corners with two outs in the eighth, but Reyes grounded back to Johnson.
Notes: Marlins 1B Jorge Cantu, who had seven RBIs in the first five games, sat out after aggravating a bruise on his left hand. Florida manager Fredi Gonzalez said he expects Cantu back in the lineup for the team's next game Tuesday at Atlanta. ... The crowd of 18,104 included former Mets ace Dwight Gooden, who is also expected to be on hand Monday night for opening ceremonies at Citi Field.
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