Alonso's home run over the left-center field wall against Miami reliever Jimmy Yacabonis (0-1) snapped a 3-3 tie. It was Alonso's NL-leading 22nd homer of the season and 14th multihomer game of his career
"I hadn't seen him at all this year prior to (Friday) and I had a really difficult time picking up his release point," said Alonso, who struck out against Yacabonis in the series opener. "Thankfully, I took a lesson from (Friday's) at bat and applied it today; saw the ball a little bit better and saw the window where the ball was coming out of."
New York starter Chris Bassitt pitched seven strong innings. Bassitt (6-5) allowed three runs and six hits while striking out five. Seth Lugo pitched a perfect eighth and Edwin Díaz struck out the three batters he faced in the ninth for his 16th save.
"I don't try to worry about the offense and what they do," Bassitt said. "Obviously, run support helps, but overall you try to treat the game as 0-0."
The Marlins erased a 3-0 deficit on Jesús Sánchez's two-run homer in the fourth and Bryan De La Cruz's solo shot in the fifth.
Alonso gave the Mets an early advantage with his homer against Miami starter Trevor Rogers in the second inning. Initially, Alonso thought the shot had not cleared the right-field wall and stopped at second before resuming his trot.
"He doesn't dwell on past successes and failures," Mets manager Buck Showalter said. "He keeps grinding with it. I think that's the common denominator of guys who drive in runs and do the things that Pete does."
The Mets padded their lead on Mark Canha's RBI groundout and Eduardo Escobar's run scoring single in the fourth.
Rogers was lifted after surrendering one-out singles to Nimmo, Marte and Lindor to load the bases in the fifth. The left-hander allowed three runs, seven hits, walked one and struck out five. He has not completed six innings since April 28.
"I thought Trevor threw the ball good," Marlins manager Don Mattingly said. "He was aggressive with his fastball. He threw good breaking balls and good changeups."
Zach Pop relieved Rogers and retired Alonso on a pop out to first and struck out Canha. Marlins relievers had thrown 9 2/3 scoreless innings until Alonso's second homer.
The Marlins settled for two runs in the fourth with Sánchez's homer. A third run was negated after New York right fielder Marte threw out Garrett Cooper at third. Cooper led off with a single and attempted to reach third on Jesús Aguilar's single to right.
"I thought this was one of our best defensive games of the year," Showalter said.
The game had additional significance for Marlins second baseman Jazz Chisholm Jr. because the club promoted it as Bahamian Heritage Day. Chisholm was at risk of missing the game after back spasms forced him to exit early Friday, but he recovered sufficiently and had a double Saturday. The Bahamanian star had 100 guests on his ticket list.
"For sure. I heard everybody in the stands," Chisholm said. "I heard my grandma. I think I saw her do that wheel thing when I hit the double. It was great today, just to have everyone here."
Mets: RHP Max Scherzer (oblique strain) will make another rehab start at one of the club's minor league affiliates early next week. There was speculation Scherzer would be activated from the injured list and start the series finale Sunday. ... INF-OF Jeff McNeill (right hamstring tightness) was not in the lineup for the fourth consecutive game. ... RHP Colin Holderman (right shoulder impingement) will throw in a rehab appearance Sunday at Triple-A Syracuse.
Marlins: INF Miguel Rojas returned to the lineup after sitting out Friday because of a bone bruise in his right foot. ... LHP Jesús Luzardo (left forearm strain) is throwing from 105 feet.