Jayson Werth hit a tying three-run homer off Fernandez after Miami Marlins catcher Jarrod Saltalamacchia committed two errors in the sixth inning, and the Nationals went on to win 6-3 Wednesday night.
''Tonight was good for us against a really tough pitcher,'' Nationals manager Matt Williams said. ''He's an animal, one of the best pitchers in all of baseball.''
After the Nationals overcame a 3-0 deficit, pinch-hitter Zach Walters broke a tie in the eighth inning with his second career homer - and his second in as many nights.
Washington took the rubber game of the three-game series despite being without four starters, including Bryce Harper, a late scratch because of a tight left quadriceps that has bothered him since Friday.
Harper is expected to be back in the lineup Thursday when the Nationals begin an 11-game homestand against St. Louis.
Fernandez, betrayed by his defense, departed for a pinch-hitter after seven innings. He allowed four hits and three runs, all unearned, with 10 strikeouts and no walks.
The Marlins' precocious ace allowed only one baserunner in the first five innings, but Saltalamacchia's throwing error put runners at first and third with nobody out in the sixth. Fernandez retired the next two batters before Werth stepped to the plate.
''I thought Jose was going to pitch himself out of that,'' Miami manager Mike Redmond said. ''He made some great pitches, then just made a mistake and the guy hit it out.''
Werth's homer, his third of the season, tied the score at 3.
''I got beat,'' Fernandez said of his matchup with Werth. ''It's part of the game. Obviously not what I wanted to happen, but we learn from it.''
Walters led off the eighth with the Nationals' first pinch-hit homer this year, which came against Mike Dunn (0-2). That raised Walters' slugging percentage to 2.000.
''Luck of the draw,'' the rookie said of his fast start.
Ian Desmond added a two-run single.
Tanner Roark allowed three runs in 6 1/3 innings, and the bullpen pitched the final 2 2/3 innings without allowing a runner. Drew Storen (1-0) got the final two outs in the seventh, and Rafael Soriano pitched the ninth for his third save in as many chances.
Washington improved to 5-1 against the Marlins this year and 14-3 against them since July. Winning the series was especially sweet for the Nationals after they were swept last weekend at Atlanta.
''The way the road trip started, to get two out of three here is good,'' Werth said.
Miami's Derek Dietrich hit a tape-measure three-run homer, his third. The Marlins have homered in eight consecutive games after finishing last in the majors in home runs in 2013.
Giancarlo Stanton, baseball's RBI leader, went 0 for 4, including two at-bats with runners in scoring position.
Fernandez remained 11-0 at home and became only the third major league pitcher since 1914 to go unbeaten in his first 18 home starts, according to STATS. And he appeared headed for a victory until the sixth.
After Jose Lobaton led off with a double, Saltalamacchia made an ill-advised throw to third on a bunt, and both runners were safe when the throw was errant. With one out, Saltalamacchia dropped a pop foul for another error that forced Fernandez to throw extra pitches.
Werth's homer deflected off the hands of a fan in the first row of the right-field seats. The ruling was upheld by a replay review that took only 22 seconds.
''We have the ability to come back because guys grind at-bats and never give up,'' Williams said.
Nationals OF Denard Span (concussion) is expected to begin a rehabilitation assignment Thursday and may rejoin the team Saturday. ... Washington RHP Doug Fister (back muscle) is scheduled to pitch two innings Thursday in an extended spring training game in Florida. He'll pitch at least twice more after that before joining the rotation, perhaps in early May. ... Jones came into the game leading the majors with 24 strikeouts, but didn't fan in this one. ... The Nationals begin their homestand Thursday against St. Louis with Taylor Jordan (0-1, 4.76) slated to pitch against Adam Wainwright (2-1, 2.57). ... The Seattle Mariners visit Miami for only the second time, and the first time since 2005, to begin a three-game series Friday.