Washington's Roger Bernadina hit a three-run homer off Johnson in the second inning.
"Obviously (it wasn't) very good, but it's spring training," Johnson said. "That's good at least."
Johnson had a 2-2 count on Washington's Ryan Zimmerman with two outs in the bottom of the second inning when he was pulled by manager Edwin Rodriguez after throwing his 58th pitch. The Marlins' expected opening day pitcher was scheduled to throw three innings, but had a pitch limit of 55.
"We're just happy to see J.J. on the mound," Marlins manager Edwin Rodriguez said. "He was healthy. His velocity was fine. There's no concern about J.J."
The right-hander was making his first start since Sept. 4 of last season when he was shut down due to back and shoulder issues. He threw 1 2/3 innings Wednesday, giving up five runs, four earned, on five hits.
"I threw all my pitches," Johnson said. "They were kind of here and there. I would throw one good one, one bad one, one good one ... two bad ones, three bad ones. That's what we're out here doing, getting it right."
Washington starter John Lannan retired the first six batters he faced before surrendering two runs on three hits in the third.
"My changeup felt good, my sinker was helped out by the wind a little bit, but it was good facing hitters," the left-hander said.
Rick Ankiel, in a three-way contest to win the starting left-field job, made a good impression, running the bases well and hitting a solo home run in the seventh inning.
Washington is now 3-0 to start the spring and a number of players have noticed a difference in the clubhouse with the addition of veterans like outfielders Jayson Werth and Matt Stairs and first baseman Adam LaRoche.
"These guys really want to win," Lannan said. "We're sick of losing. We've got some guys who have won in the past couple of years and they're bringing that attitude with them. I think it's contagious, just as if losing is contagious. Right now, I think we have a winning attitude. I know it's still early, but it's a good sign."
Washington RHP Stephen Strasburg, rehabbing from Tommy John surgery, threw the ball from about 75 feet before Wednesday's game and reported he felt fine. Though he appeared to be throwing the ball harder than when camp started, the team is being very cautious with him to go too far just yet. "They don't want me to put too much pressure on it," Strasburg said. "They just want it to be a fluid throw. I'm just going out there nice, free and easy. I'm not lobbing the ball, but at the same time, I'm not trying to play burnout or anything." ... The Nationals have confirmed that they are exploring options to relocate their spring training operations, "for baseball reasons, primarily stemming from travel and proximity issues," team spokesman John Dever said. The Nationals' lease at Space Coast Stadium runs until 2017. ... Marlins RHP Ricky Nolasco (jammed thumb) reported no problems a day after his first bullpen of the spring. He is expected to throw two more and possibly a simulated game before making his first spring start March 13. ... Florida OF Mike Stanton's strained right quadriceps is improving, but he could still miss several weeks. Rodriguez said it was likely Stanton could still be ready to start the season, provided he can return to face live pitching at least 10 days before the end of spring training. ... Nationals RHP Cla Meredith had Tommy John surgery on his right elbow Wednesday.