Miami took a 5-0 lead through three innings thanks, in part, to a two-run home run by Logan Morrison and went on push the Nationals closer to elimination in the National League East pennant chase.
Although Atlanta lost Friday, the setback for the second-place Nationals reduced the Braves' magic number for clinching the division title to nine.
Fernandez (11-6) struck out nine, walked two and did not give up a hit until pinch-hitter Zach Walters reached on a one-out single in the sixth. The only other Washington hit came off reliever Chad Qualls in the eighth.
Giancarlo Stanton drove in three of Miami's runs, two of them with a first-inning single. He also hit a home run in the eighth.
The loss went to Dan Haren (8-3), who allowed five runs on six hits in just three innings.