The loss was the Marlins' third straight, and it knocked them 10 games behind the Nationals in the National League East.
Jordan Zimmermann silenced the Marlins for six shutout innings, striking out six.
In 5 1/3 innings, Johnson gave up five runs on 11 hits, which matched his career high. The right-hander, now 8-1 lifetime against Washington, previously gave up 11 hits on April 11 at Phillies.
"I don't think he was very sharp at all," manager Ozzie Guillen said of Johnson, who fell to 5-6 on the season. "He wasn't throwing the ball where he wanted to. He was a little bit off today, a little bit off."
From the first inning it was a struggle for Johnson. The Nationals stranded Bryce Harper at third base in the first, but they cashed in with a run in the second. Adam LaRoche doubled and scored on Ian Desmond's RBI single to right.
The rest of the night didn't go much better, as the Marlins were unable to generate early momentum coming out of the All-Star break.
"We couldn't put it together because Zimmermann was throwing the ball pretty good," Guillen said. "I think today we took like another All-Star break day. Hopefully we come back tomorrow and start swinging the bat better."
After dropping back-to-back games in St. Louis before the break, the Marlins have now stumbled to a three-game skid.
"I think we put ourselves in position where I think every series is big, regardless of who it is," said catcher John Buck, who drove in the team's only run. "We have three games left. We need to go out and try to win the series."
The way the Nationals pitched made the Marlins look flat. But Washington also played with energy from the first inning. A telling play came in the opening frame when Harper was on second base. The 19-year-old rookie caught Miami's left side of the infield napping.
Third baseman Hanley Ramirez and shortstop Jose Reyes were talking, and Johnson had the ball with his head down on the mound. Seeing an opening, Harper stole third.
"Heads-up play for Harper, that's all," Guillen said. "I think everybody's heads were down, and he took advantage of that."
In the third inning, Washington struck again, going up 3-0 on Zimmerman's two-run homer.
"I didn't go out there and go deep into the game and give us a chance to win," Johnson said. "Forget about those first three runs. I've got to go out there and get those last two outs, but I didn't do it."
The Nationals took advantage of the Marlins' inability to turn a double play on Harper's grounder to second. While Miami forced Steve Lombardozzi out at second, Reyes' throw to first was off the mark, allowing Harper to reach. On a 3-1 count, Zimmerman blasted a drive to left-center estimated at 399 feet.
It was Zimmerman's first career home run off Johnson, coming on his 34th at-bat.
"It was a little slider, cutter thing he was throwing," Zimmerman said. "He's good. He's always good. He's not a fun guy to face. I guess you could say he made a mistake, and I put a good swing on it."
The home run was just part of a rough night in which Johnson had to battle for 99 pitches in less than six innings.
"Pretty bad," Johnson said. "Not the way you want to start the second half. We'll come back tomorrow and try to win the game."
Washington had at least one hit in every inning off Johnson, who exited with one out in the sixth. LaRoche again did some damage in the sixth, starting the inning with a single. Desmond dropped down a bunt single, and with one out, Flores floated a two-run single to left, ending Johnson's night.
Miami got on the board in the seventh on Buck's RBI single to right off Henry Rodriguez. The Marlins had a chance for a bigger inning, but with runners on the corners and one out, Michael Gonzalez got pinch-hitter Austin Kearns to line back to the mound and into an inning-ending double play.
The Marlins understand the magnitude of the four-game series against the first-place Nats now that they are 41-45 overall.
"We all know this is a big series for us," Guillen said. "Everybody knows. Hopefully we play better tomorrow. We know they're playing pretty good baseball, they're pitching well.
"For us, this is not a do-or-die situation, but it would be nice to win a couple of games against them."