Fernandez couldn't do it with his arm a day later.
"That's how baseball is," the 23-year-old right-hander said. "Baseball doesn't make much sense."
Fernandez gave up more runs than he had in his previous nine starts and the Braves won 9-1 behind home runs from Freddie Freeman and Jace Peterson on Saturday.
Freeman hit a two-run homer in the first inning and Peterson added a three-run shot in the sixth after that inning was prolonged by an error.
"He's one of the best pitchers in the game, so when you can get a win against a guy like that it's huge," Peterson said.
A seven-run sixth inning knocked out Fernandez (10-4), who gave up eight hits and was charged with all nine runs (six earned).
"This game always finds a way to remind you how tough it is," Fernandez said.
Veteran right-hander Lucas Harrell, promoted by Atlanta from Triple-A Gwinnett as a fill-in starter for traded Bud Norris, was as good as Fernandez was bad.
Harrell, who pitched in Korea last year, allowed three hits and a run in six innings, striking out five and walking one.
"It's a really great feeling," the 31-year-old said. "It's been a long road to get back. I felt like I've worked really hard."
It was the first start in the majors for Harrell (1-0) since April 15, 2014, when he was with Houston. He had an 11-11 record and 3.76 ERA for the Astros in 2012 after breaking in with the Chicago White Sox in 2010.
Harrell, who was effective with his cutter and sinker against the Marlins, signed on May 20 with the Braves after being released by the Detroit organization and was 2-1 with a 2.81 ERA for Gwinnett.
Atlanta (28-53) claimed its eighth victory in 11 games against the Marlins (42-39) this season. The Braves have a winning record against no other team.
Fernandez struck out eight and his only walk was intentional, but he threw three wild pitches in the uncharacteristic outing.
Peterson led off the first inning with a double, extending his career-best hitting streak to 13 games, and Freeman turned around a 98 mph fastball from Fernandez for a homer into the center-field seats.
It was Freeman's 14th homer of the season and the 11th of his career against Miami. He finished 3-for-4 to raise his average to .289.
The Marlins scored in the third inning on a single by Derek Dietrich and two-out triple by Ichiro Suzuki, who moved within 11 hits of the 3,000-hit milestone in the United States.
Fernandez, though, couldn't make it out of the sixth inning, when the Braves sent 10 batters to the plate.
An error by Chris Johnson, who came in at first base after Justin Bour sprained his right ankle, allowed another run to score and Peterson followed an out later with his three-run homer off a changeup to chase Fernandez.
Fernandez allowed only one hit in seven scoreless innings in his previous start against the Braves this season and was 4-1 with a 2.15 ERA against them.
Did his late-night heroics Friday have any bearing on his subpar performance Saturday?
"I'm sure it is emotional to do something like that and he is an emotional kid," Marlins manager Don Mattingly said. "He probably had a little trouble getting to sleep. So it could have had something to do with it."
Fernandez downplayed that possibility.
"I went back, got to sleep," he said. "Everything was normal. My regular routine."
NOTES: The four-game series concludes Sunday night at Fort Bragg, N.C., in the first professional game on an active U.S. military base. ... Braves RHP Matt Wisler (3-7, 4.14 ERA) is scheduled to start against Marlins LHP Adam Conley (4-5, 3.90 ERA). ... The Braves optioned RHP Casey Kelly (0-3, 5.82 ERA) to Triple-A Gwinnett after he took the 12th-inning loss Friday. ... RF Giancarlo Stanton and SS Adeiny Hechavarria were out of the Miami lineup, but both came in late. ... Braves CF Ender Inciarte hopes to play Sunday after suffering only a slight groin strain Friday. ... SS Kevin Maitan, a 16-year-old from Venezuela considered the No. 1 international amateur prospect, signed with the Braves for a bonus of $4.25 million.