Fernandez struck out nine in seven scoreless innings and provided the lift the Marlins need to claim a 2-0 victory over the Phillies in front of 40,091.
Marcell Ozuna and Chris Valaika each homered, providing all the offense Fernandez needed to collect his first big league victory.
Fernandez, Mike Dunn and Steve Cishek combined on the one-hit shutout, which snapped Miami's three-game losing streak.
For days, the Marlins' top prospect was telling pitching coach Chuck Hernandez that he was looking forward to this start.
"Chuck told me he couldn't wait to pitch tonight," Miami manager Mike Redmond said. "You hope all your guys say that. When he says it, he really means it. He really couldn't wait to go out there and try to help us get a win. He threw some nasty pitches tonight, and he really held a tremendous lineup in check."
The Marlins' last one-hit shutout was a complete game by Anibal Sanchez at Pittsburgh on Sept. 10, 2011.
"It is amazing to get a win," said Fernandez, the No. 7 prospect on MLB.com's Top 100 Prospects list. "But it's more important for the team than me. I knew sooner or later, I was going to get it. It was just fun. Everybody is in a good mood here. It was fun."
Making his sixth start, the seven innings and nine strikeouts were both career highs. Fernandez also limited the Phillies to one hit, a one-out single by Freddy Galvis in the first inning. He then retired 17 straight before walking Galvis to open the seventh inning.
Retiring 17 in a row tied a club record by a rookie. It's been done five times, with Dontrelle Willis last doing it on June 16, 2003.
For the second time, Fernandez has been impressive against the Phillies. On April 13 at Marlins Park, he held them scoreless for six innings, striking out five.
"They're a great lineup," the rookie said. "They've got some great hitters that I respect a lot. I go out there and I try to make pitch by pitch the best ones I can. It's just fun, every fifth day you get to go out there and have fun."
Fernandez simply overpowered the Phillies. His dominance was reflected in how he fared against Chase Utley and Ryan Howard. The two were 0-for-6 with five strikeouts. Howard fanned all three times he faced Fernandez.
"That doesn't happen very often," Redmond said. "Anybody that gets through the heart of this order, you've got to execute your pitches. To Howard, it seemed like he had him out front all night long. He just didn't have a feel for when that breaking ball was coming or when that fastball was coming."
The Marlins now have a chance to split the four-game series on Sunday.
Fernandez needed to be on top of his game because Phillies lefty Cole Hamels also was impressive, allowing two runs on four hits with six strikeouts in eight innings.
"He's really impressive," Hamels said of the Miami right-hander. "He's going to be a really great pitcher for a really long time because he came up early and he's going to learn how to pitch, if he doesn't already know how to.
"He's got a power heater, power curveball, pretty good changeup. And he's not afraid. And that's ultimately what separates him. He's not afraid to throw any pitch at any time. He definitely challenges hitters, and that's going to help him out in the long run. He's going to put up pretty good numbers in his career."
Miami used the long ball to get the best of Hamels, with Ozuna providing the first blast.
Promoted from Double-A Jacksonville on Tuesday after Giancarlo Stanton went on the disabled list, Ozuna has hit safely in all five games he's played in the big leagues.
A native of the Dominican Republic, Ozuna has his father, sister and nephew in Philadelphia for the series. They had something to cheer about.
"I'm pretty happy, because my family, they came to see me," Ozuna said. "It's [surreal]. That's your blood. I got the ball."
Leading off the second inning, Ozuna turned on Hamels' first pitch and connected on his first MLB home run. In the dugout, his teammates offered him support and a lofty goal.
"Everybody said, 'Congratulations,'" Ozuna said. "They said, 'That's No. 1, 500 more.' I was pretty happy."