But they misjudged the strength of Marcell Ozuna's arm.
"It's pretty surprising. Hats off to Ozuna," Nieuwenhuis said. "He made a great throw. There's no other way to put it."
Even Ozuna thought the Mets had tied the game.
"I didn't think I had a chance to get him out, but I was going to throw it no matter what," Ozuna said.
Ozuna also threw out David Wright to end the eighth after the Mets cut the deficit to 3-2.
"I can't remember seeing a game decided by two great throws from a left fielder and two great tags from the catcher to end the game," Marlins manager Mike Redmond said. "That's pretty amazing."
Henderson Alvarez (4-3) pitched 6 1/3 scoreless innings, allowing seven hits without a walk, and struck out five. In his past six starts, he is 2-0 with a 0.68 ERA, which leads the majors since May 22.
"It was a good start for myself. All my pitches were working. Now it's about keeping going forward," Alvarez said.
Steve Cishek allowed a double to Nieuwenhuis to open the ninth, but earned his 17th save in 18 chances when Ozuna's throw landed in catcher Jarrod Saltalamacchia's glove for his fourth assist of the season.
"He started at the Clevelander, so I didn't think he had a shot, but he started running in," Saltalamacchia said. "Once he got closer I knew he had a chance, but that's a tough throw, big moment like that. You tend to do too much. He made a perfect throw."
Mets starter Daisuke Matsuzaka (3-1) allowed one run and six hits in 5 1/3 innings. He struck out four.
"I felt good today, and just going off our last time off of Alvarez, I knew it was going to be a close game -- a one or two-run game -- so I knew I couldn't give up too many runs," Matsuzaka said. "One run ended up making a difference."
Adeiny Hechavarria drove in two runs, and Saltalamacchia hit two doubles for the Marlins, who won their major league-best 17th one-run game of the season despite going 1 for 11 with runners in scoring position.
"It was nice to win that one," Redmond said. "We needed to win that one."
Six of the eight games between these clubs this season have been decided by one run.
New York had a two-game winning streak snapped.
With the Mets trailing 3-0 in the eighth, Wright hit an RBI single off Kevin Gregg. Two batters later, with Mike Dunn pitching, pinch-hitter Eric Campbell singled to left field to make it 3-2. Wright was thrown out at the plate as he tried to score on the hit.
"I got thrown out by about 10 feet, so it wasn't a real close play," Wright said, "but at the same time we kind of thought that he was blocking (the plate) and apparently they thought he wasn't."
Mets manager Terry Collins challenged the play, taking up the argument that Wright was blocked from getting to the plate.
"When you saw replays, his foot had pretty much that whole side blocked," Collins said. "The over-the-top view, I don't know. You don't ever get an explanation. All they say is the play stands.
"You don't ever get an explanation or why they ruled it, and the umpires are as confused as anybody."
Rafael Furcal led off of the game for the Marlins with a triple off the right-field fence and scored on a groundout by Hechavarria. It was Furcal's first extra-base hit of the season in 30 at-bats and first leadoff triple since June 11, 2010, against the Angels when he played for the Dodgers.
"I knew that was the only run I could give up the rest of my outing," Matsuzaka said.
"It surprised them a little bit that he took off there with a left-hand hitter," Redmond said. "He was being aggressive and took advantage of a bad throw. That was a huge run for us."
The Marlins extended their lead to 3-0 later in the inning when Wright attempted to bare-hand a grounder hit by Hechavarria, but the ball bounced past him, allowing Justin Bour to score.
Wright was originally charged with an error, but it was later changed to a hit.
Mets SS Ruben Tejada took a base hit away from Casey McGehee in the eighth inning when he made a diving stop to his left, spun on the ground, and threw to first from his knees. ... Wright has a 10-game hitting streak at Marlins Park. ... Miami will send RHP Tom Koehler (5-5, 3.84) to the mound on Saturday. New York will counter with RHP Jacob deGrom (0-4, 4.39).