El Duque limited Washington to just three hits and one run -- a game-tying homer to right field by Felipe Lopez, his sixth dinger of the season -- while striking out eight batters and walking two.
"I've seen him many, many times, and he never ceases to amaze me," manager Willie Randolph said. "When he's on his game and hitting his spots, throwing his breaking ball, not many guys can do what he does."
The outing marked the third win in four starts for Hernandez since the All-Star break. Hernandez posted a 2.42 ERA in his last four starts, and he hasn't allowed more than one run in eight of his last 17 games.
"I feel good," Hernandez said. "I'm happy. My team lost [on Friday] and I helped them win a little bit today. ... I moved my ball very good today. My slider was very good and my control was very good for me."
Amazin' as Hernandez was, the Mets bullpen was just as good. Billy Wagner recorded his 24th save of the season, moving him into sole possession of seventh place on baseball's all-time saves list with 348 in his career. Wagner has not allowed a run in 17 innings since June 15.
Wagner took the mound with the Mets ahead, 3-1, following a scoreless inning from Aaron Heilman.
"[They are] a tough team," Wagner said. "The record says they're not that good, but they give us fits every game. It was a good win. Duque and Aaron did their jobs, and we got the offense going."
Heilman struck out one in the eighth, holding Washington without a run in his fourth consecutive scoreless appearance. Lately, the right-hander said, he has been able to locate his fastball more easily as he's found his niche in the bullpen.
"It's a combination of throwing the ball better and getting a lot of consistent work, which I think helps anybody," Heilman said.
The game was knotted at 1 until the seventh inning, when Carlos Delgado and Ruben Gotay hit RBI singles off reliever Saul Rivera to give the Mets the two-run lead.
Gotay knocked the ball over second baseman D'Angelo Jimenez's head, sending Jose Reyes home to put the Mets ahead, 2-1. Delgado's shot to right field scored Gotay, tacking another run on the board.
"Maybe I get more concentrated in that situation," Gotay said. "I'm just trying to get the job done. Maybe I did today, but it's not enough. I just need to keep working hard."
The 24-year-old second baseman had impressive at-bats, going 2-for-4, including the game-winning single, but was rusty on defense. In the ninth inning, Gotay missed turning a game-ending double play with a shaky throw to first.
"He's a young player, doesn't play a lot, so his rhythm is not always there," Randolph said. "He's been pulling the ball a little bit, but he has a good arm. That's just something he needs to continue to work on, I'm not concerned about it."
Nationals starter Tim Redding limited the Mets to just one run on five hits, walking four over six innings and tying his career high with eight strikeouts. Lastings Milledge hit an RBI double to left field off the right-hander in the fourth inning to bring home Delgado for the Mets' first run.
The double extended Milledge's hitting streak to seven games, and he is batting .444 during that stretch. The outfielder also suffered his third hit by pitch in four games.
"I've been hit everywhere," Milledge said. "I just got to stay in there and keep plugging. They're trying to move me off the plate. I have great plate coverage, so they try to move me off the plate too, so I can't take their slider away."
But when it comes to his battered left arm, Milledge doesn't mind so much. A Mets' win is the best type of Band-Aid.
"Definitely," Milledge said. "I'll take one for the team. It's good, we got off to a good start today."
Lauren Kobylarz is an associate reporter at MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.