The 6-foot-7 right-hander threw 17 pitches before rain halted play in the second inning. After that long delay, he threw 56 more pitches and was lifted after five innings on a night he didn't give up a run and scattered three hits.
"If there is a little strain, he won't pitch at all the rest of the year," manager Joe Girardi said Tuesday. "He played catch [on Monday] and he still felt a little stiff, so I'm not going to start him [Saturday]. It's not worth it."
Brian Moehler, who filled Johnson's rotation spot in Monday's 4-0 loss to the Mets at Shea Stadium, now will start on Saturday at Philadelphia.
Johnson tried to have a light catch on Monday, but his forearm didn't loosen up. An MRI was taken to see the extent of the discomfort.
Initially, the team said Johnson was bothered by a cramp in the muscle of the forearm.
Johnson is expected to rejoin the team in New York on Wednesday.
"He's frustrated because he wants to pitch," Girardi said.
Johnson is an NL Rookie of the Year candidate. The Tulsa, Okla., native is 12-7 with a 3.10 ERA. His ERA is fifth overall in the Major Leagues.
He has logged 157 innings, and to rank among the league leaders in ERA, he would have to throw at least 162 innings.
Johnson has appeared in 31 games with 24 starts. He opened the season working out of the bullpen. About the time he joined the rotation is when the Marlins began to show tremendous improvement as a team.
As a starter, Johnson is 11-5 with a 3.03 ERA, throwing 145 1/3 innings.
Pinto's progress: At 6-foot-4, lefty Renyel Pinto has an imposing presence on the mound. The 24-year-old, acquired from the Cubs as part of the Juan Pierre trade, has been put in a tough spot with the Marlins.
He's bounced up and down between Triple-A Albuquerque and the Marlins.
For the Isotopes, he was 8-2 with a 3.40 ERA in 18 starts, with one complete game. Since the Marlins rotation was solidified, Pinto has been used in long-relief, and the past few weeks, the Venezuelan native has seen action in a setup role.
Getting a taste of the big leagues now should help Pinto next year, where he will go into Spring Training as a candidate to either start or relieve. He provides a second lefty, to go along with Taylor Tankersley.
"He's got three pitches, but the key for him is throwing strikes," Girardi said.
Pinto has as many walks as innings pitched, 24. And he's struck out 26.
"I've treated him as one of the short guys [lately]," Girardi said. "It's a role I think he can definitely help us in."
The Marlins started the season with no lefty relievers, which limited Girardi's options until Tankersley emerged as a reliable late-inning pitcher in early June.
Franco at third: After clinching their first NL East title since 1988, the Mets gave their regulars a break from starting Tuesday.
One interesting move is starting 48-year-old Julio Franco at third base. The last time Franco started at third was in 1982.
To put that into perspective, consider in the Marlins dugout Tuesday night, 13 players were born either in 1982 or after.
Hermida's role: Jeremy Hermida, who hasn't started since Aug. 30 because of a right ankle injury, isn't likely to play the outfield in the final two weeks. But Girardi has not ruled out using the rookie right fielder as a pinch-hitter.
The left-handed-hitting Hermida has appeared twice as a pinch-hitter in September, making his last appearance on Sept. 4.
"He's not able to run 100 percent," Girardi said. "It's silly to put him out there."
Coming up: On Wednesday night, Dontrelle Willis (11-11, 3.80) takes the mound for the Marlins, while the Mets are turning to Oliver Perez (3-11, 6.61). First pitch is scheduled for 7:10 p.m. ET.