"I felt really good out there today," said deGrom, who was a late scratch from Monday's game against the Tigers due to back stiffness. "The little extra time off, skipping that one helped."
In relief of deGrom, lefty Steven Matz gave up three runs on five hits and a walk while striking out three in four innings.
The Mets were able to chase Fernandez with two outs in the fourth inning on d'Arnaud's two-run single with the bases loaded, boosting the score to 4-0. Granderson broke the game open with a two-run single off reliever Nefi Ogando.
• Edwin Jackson pitches three scoreless
Fernandez breezed through the first two innings, striking out four, and his fastball maxed at 98 mph. But in his third and fourth innings, the 23-year-old encountered trouble.
"That's baseball, it happens," said Fernandez, who finished with six strikeouts. "Obviously, you're not happy about it. I don't care if it's Spring Training or an intrasquad game, whatever it is, you've got to go out there and give your team a chance to win. I didn't do that today."
• Fernandez takes outing in stride
In the third inning, the Mets broke through for two runs. Alejandro De Aza singled to open the inning, and he scored on d'Arnaud's double to right. With one out and d'Arnaud on third, Granderson was credited with an RBI single on a sharp grounder to first. Playing in, first baseman Derek Dietrich was unable to handle the hot shot, though right fielder Giancarlo Stanton was able to throw out the eager Granderson at second.
The Marlins' one hit off deGrom was a double by Stanton to open the second inning. But Stanton wasn't able to advance, and the inning ended when deGrom struck out Jeff Mathis.
deGrom pitched in the 91-94 mph range and touched 96 in the outing.
• Justice: Mets can relax after deGrom's start
The Marlins got on the board in the sixth inning on Marcell Ozuna's RBI single off Matz. Austin Nola drove in a pair between his sixth-inning triple and ninth-inning double. Mathis and Francisco Arcia drove in the Marlins' other two runs on singles.
Up next for the Mets: David Wright will make his Grapefruit League debut Friday in a 6:10 p.m. ET game against the Nationals that will air on MLB.TV and Gameday Audio. Wright, who eased into baseball activities this spring after spending much of the offseason resting his back, will face Nationals prospect Lucas Giolito at Tradition Field. Bartolo Colon is scheduled to start for the Mets.
Up next Marlins: The Marlins travel to Lake Buena Vista, Fla., on Friday to face the Braves in a 1:05 p.m. ET tilt that will air on Gameday Audio. Lefty Chris Narveson is getting the start for Miami against right-hander Matt Wisler. Dee Gordon is among the regulars expected to be on the trip.