In a frantic finish, Ozuna threw strikes to the plate in the eighth and ninth innings, thwarting New York's chances at scoring the tying run. In both instances, the umpires reviewed the call to see if Saltalamacchia had blocked the plate.
Instant replay was used three times on the night. MLB's new collision rule was tested twice, with both rulings confirmed in Miami's favor.
"Everybody was a little frustrated at the end of the game for a variety of reasons. I'll leave it at that," Mets general manager Sandy Alderson said. "There's been confusion on other rules, including a variation on plays at the plate."
Trailing by a run in the ninth inning, Kirk Nieuwenhuis doubled to right and advanced to third on Ruben Tejada's sacrifice bunt. With one out, Marlins closer Steve Cishek had the count full to Chris Young, who lifted a fly ball to left. Initially, it appeared to have plenty of distance for the tying sacrifice fly.
Ozuna initially drifted back and then charged forward, getting as much momentum as possible to make his throw home. He collected the ball and fired a perfect throw to Saltalamacchia, and home-plate umpire Lance Barrett called Nieuwenhuis out.
The Mets challenged as the Marlins celebrated. After a review of 55 seconds, the call was confirmed.
"For me, it's all about who's watching your game," Mets manager Terry Collins said. "You might have one crew that thinks he's blocking the plate. You might have another crew that thinks he doesn't. Until there's a clear and cut decision, there's going to be challenges all the time."
Saltalamacchia let instincts take over.
"At that point, I'm just trying to do what I've done," Saltalamacchia said. "You've got to kind of let instincts take over and not take it too much in front of the plate. You've got to remember that.
"I was just sitting back, letting the ball to come to me. He gave me two good throws where I didn't have to do anything. I let the ball travel. As a catcher, that's probably one of the best feelings, knowing that you're not going to have to move left or right. He threw it right on the money for me."
The collision rule was established to protect players. Saltalamacchia came off the disabled list on Thursday after he had been out with a concussion sustained on a foul tip.
"I thought Salty was fine," Miami manager Mike Redmond said. "There's still sort of that little gray area where we're not really sure. But he had the ball well before the guys were there. And once you have the ball, you can block the plate. For me, he had the ball both instances well before the runner got there."
"He was out," Collins said. "Replays showed he was out. Rules are rules. And that's why once in a while you've got to go challenge 'em."
In the eighth inning, Ozuna threw David Wright out at the plate after Eric Campbell slapped an RBI single to left off Mike Dunn. Eric Young Jr. scored from first, but Ozuna's throw had Wright in plenty of time. Collins questioned if Saltalamacchia gave Wright enough of the plate to slide into, and a crew-chief review was initiated. It lasted one minute and 47 seconds before the call was confirmed.
"This isn't a bashing or calling out or anything," Wright said. "I got thrown out by about 10 feet, so it wasn't a real close play. But at the same time, I think we kind of thought that he was blocking it, and apparently they thought he wasn't. Like I said, it's just a little confusing. But hopefully we'll get used to it and adjust.
"It's just something you've got to get used to. You play one way your entire life and then you've got to adjust to the play. It's not necessarily a bad thing. I understand safety and health and things like that."
Ozuna, who has four outfield assists on the season, has the strongest throwing arm in the Marlins' organization.
"I never had a game where I made two throws like that," Ozuna said. "I was happy. I don't care if I didn't get a hit. I'm happy."
The plays at the plate generated the most attention after the game. But there was a significant overturn that went in New York's favor in the fourth inning.
With one out in the fourth, Jones ripped a 1-1 pitch into the right-field corner of the park, and it was initially ruled a homer.
Collins asked the umpires to review if the ball was fair or foul. The umpires review home runs, so it wasn't a Mets challenge.
Replays showed it was foul by just inches, and after the one-minute, 29-second crew-chief review, Jones' homer was taken away. Matsuzaka ended up retiring Jones on a groundout to first base.
Joe Frisaro is a reporter for MLB.com. He writes a blog, called The Fish Pond. Follow him on Twitter @JoeFrisaro. Associate reporter Maria Torres contributed to this report. This story was not subject to the approval of Major League Baseball or its clubs.