Fernandez (1-2), the Marlins' 2011 first-round draft choice out of Tampa, Fla., was making his sixth big-league start. He baffled the Phillies, setting down 17 straight batters after yielding a first-inning single to Freddy Galvis.
The 20-year-old right-hander issued one walk and struck out nine en route to the milestone win.
Mike Dunn tossed a 1-2-3 eighth and Steve Cishek notched his fourth save, competing the one-hitter as the Marlins broke a three-game skid.
Marcell Ozuna socked his first major league homer and Chris Valaika added a solo shot, providing Miami's offense.
Cole Hamels (1-4) took the loss for the Phillies despite yielding just two runs on six hits over eight innings.