The last-place Nationals also beat the NL East leaders 7-1 on Saturday night, and took two of three in the series - Washington's first series win at Citi Field since it won two of three in April 2019.
''We're going to play a lot of teams that are in playoff hunts here coming up,'' said Erick Fedde, who won for first time since June 21 and earned his first victory against the Mets in 16 appearances (11 starts).
''It's our job to play spoiler and continue to play good baseball. It's a lot of fun doing that,'' he said.
The Mets have led the NL East for 145 consecutive days, but their edge is down to one game over Atlanta. New York has scored three runs or fewer in nine of its last 14 games.
''There's always a word you use about it, whether it's a dip or a slump,'' Mets manager Buck Showalter said. ''But why is that? Because of the level they've played it. It's a break from that. And I feel confident that (will change) every time the sun comes up. But you've got to make it happen. You can't just will it.''
Luis Garcia had an RBI single in the first inning, then the Nationals scored four unearned runs against Carlos Carrasco (13-6) in the third after second baseman Jeff McNeil's error led to two-run singles by Keibert Ruiz and Ildemaro Vargas.
Carrasco, activated from the injured list prior to the game after missing more than two weeks due to a strained left oblique, was charged with one earned run in 2 2/3 innings.
Hernandez, who had a career-high 21 homers last season, ended his drought by hitting a no-doubt, two-run shot into second deck in right field in the fifth. The drive was his first since Aug. 26, 2021, a span of 155 games.
''Extremely happy to get the first one out of the way,'' Hernandez said through an interpreter. ''Hopefully I find some more consistency the rest of the season and hit a few more.''
Upon finishing his home run trot, Hernandez was given the silent treatment by teammates before they finally mobbed him in the dugout following Trevor Williams' first pitch to Vargas.
Entering Sunday, only the Los Angeles Angels' Magneuris Sierra (223 games) and the Cleveland Guardians' Myles Straw (157 games) had gone longer without homering among active players.
''I went over and started screaming at him and then the teammates came over,'' Nationals manager Dave Martinez said with a grin. ''Man, he's waited all year for that one and I'm happy for him.''
Hernandez leads the Nationals in hits (122), doubles (26) and plate appearances (547) but has played in just three of the last eight games for rebuilding Washington. He made his first two big league appearances in left field Saturday and Sunday.
''He's changed roles,'' Martinez said. ''And he's gone out there, he's accepted it, he's done well. He's a veteran guy and a true professional.''
Lane Thomas, who started at all three outfield spots this weekend, had two hits and drew a walk for the Nationals. He finished the series by reaching base in seven of his final nine appearances, a stretch that included five straight hits bridging Saturday and Sunday.
Fedde (6-9) gave up one run - McNeil's second-inning sacrifice fly - over six innings.
Williams relieved Carrasco and pitched 4 1/3 innings. The homer by Hernandez snapped Williams' scoreless streak - which dated back to July 7 and spanned eight appearances, including two starts - at 26 innings.
Martinez said the club would employ a six-man rotation this week in order to get Patrick Corbin, who threw seven innings Saturday for the first time since July 4, an extra day of rest. Cory Abbott, who hasn't started since Aug. 17, is scheduled to rejoin the rotation and start Wednesday. Abbott tossed the ninth inning Sunday.
The Mets honored retiring scout Jim Reeves by having him throw out the first pitch. Reeves, who is based in the Pacific Northwest and signed Wyoming-born outfielder Brandon Nimmo and Colorado-born pitcher David Peterson, threw the pitch to Peterson. Nimmo then bounded out of the dugout and hugged Reeves before the three posed for a picture near home plate.
Nationals: RHP Victor Arano (right shoulder strain) was placed on the 15-day injured list, retroactive to Friday. RHP Andres Machado was recalled from Triple-A Rochester. . DH Nelson Cruz (right knee contusion) missed a second straight game.
Mets: RHP Max Scherzer (left side fatigue) said he felt fine a day after exiting after five innings and 67 pitches. Scherzer, whose next start is scheduled for Friday, missed almost seven weeks earlier this season with a left oblique injury. Of this fatigue, Scherzer offered a chuckle. ''It's kind of like everywhere except the oblique,'' he said Sunday morning. . INF Luis Guillorme (left groin) is scheduled to begin a rehab assignment Tuesday. . To make room for Carrasco on the active roster, the Mets optioned RHP Adonis Medina to Triple-A Syracuse.
Nationals: A 10-game road trip continues as RHP Anibal Sanchez (1-5, 5.05 ERA), fresh off earning his first win Wednesday, starts the opener of a four-game series against the St. Louis Cardinals. Sanchez last pitched at Busch Stadium in the 2019 NL Championship Series, when he carried a no-hitter into the eighth inning in Game 1.
Mets: RHP Taijuan Walker (10-3, 3.45 ERA) starts Monday afternoon in the first game of a three-game series at the Pittsburgh Pirates. Walker hasn't received a decision in any of his last three starts.
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