In his previous start on Monday against the Mets at Citi Field, the hard-throwing right-hander was clocked mostly at 91 mph, instead of his customary 95-96.
Another signal occurred on Thursday, when Johnson threw his between-starts bullpen session. Afterward, he felt discomfort, so he approached the coaching staff. The two-time All-Star then underwent an MRI on Friday, which revealed right shoulder inflammation.
As a precautionary move, the Marlins on Saturday placed their ace on the 15-day disabled list, retroactive to May 17.
Right-hander Jay Buente had his contract selected from Triple-A New Orleans, and he will start in place of Johnson against the Rays on Sunday at Sun Life Stadium. Buente was scratched from his scheduled start on Friday with New Orleans once it was determined Johnson would go on the DL.
For Florida, it's a big blow -- an injury to its top starting pitcher with the team 1 1/2 games behind the Phillies in the National League East.
"You don't replace Josh Johnson," manager Edwin Rodriguez said. "Hopefully, you'll send somebody out there who can keep you in the game for five innings, and after that, we take it over from the bullpen. To replace Josh Johnson, right now, it's hard to do."
One of the dominant pitchers in the game, Johnson and Jaime Garcia of the Cardinals each have a 1.64 ERA, which is tied for best in the big leagues.
Johnson is 3-1, and he's thrown 60 1/3 innings over nine starts.
For at least a couple of days, Johnson has been shut down from throwing. He will be re-evaluated on Tuesday, and the organization is hopeful that Johnson will be reinstated to pitch on June 1 at Arizona.
For now, that's the best-case scenario.
"You never know with this kind of stuff," said Johnson, an All-Star the past two seasons. "You just are making sure you get all the inflammation out, and that kind of stuff. From there, it should be fine."
Johnson, the NL Pitcher of the Month in April, said he has dealt with shoulder tightness since Spring Training, but he's been able to loosen up to be effective.
Last September, Johnson was shut down due to a strained back muscle. At the time, he also experienced some shoulder stiffness. He isn't sure if the discomfort now is the same as then because he didn't test the shoulder by throwing at the end of the 2010 season.
"I never tried to throw on it," Johnson said. "Last year, after six or seven days -- my shoulder felt fine after that."
Even though he missed the final three weeks of last season, Johnson hadn't technically been placed on the disabled list since 2008, when he returned in July after undergoing Tommy John surgery in 2007.
Buente, who has pitched in the big leagues as a reliever, is expected to fill in the rotation until Johnson returns. At New Orleans, Buente was 3-0 with a 1.94 ERA in 10 appearances, including five starts.
"It's impossible to replace [Johnson]," Buente said. "I'm just going to go out and be the pitcher that I've been up to this point."
The Marlins are off on Monday, and Rodriguez didn't rule out reshuffling the rotation when the team goes on the road beginning on Tuesday at San Francisco.
With Johnson out for a minimum of two starts, the Marlins will look for the rest of the rotation to step up. Of late, Anibal Sanchez, who started on Friday against the Rays, has been pitching like an ace.
Sanchez is 13th in NL starters ERA at 3.02, Ricky Nolasco is 3-0 with a 3.32 ERA, and Chris Volstad and Javier Vazquez round out the rotation.
"Josh is a big part of our team and our success," catcher John Buck said. "Trying to look at the positive -- with Anibal, I feel very confident that if we don't have Josh, Anibal can step up in that role right now, with the way he's throwing the ball. He can kind of be that second stopper.
"They complement each other well. That kind of helps break up a series, and have that other stopper later in the rotation. I feel like [Sanchez] can pick up in the slack."
Buck also is confident that Volstad, who is 2-3 with a 5.73 ERA, is turning the corner.
"I truly believe Vollie is getting better," Buck said. "You can see his outings getting better and better. I've said it since Spring Training that he has underachieved. Now, I'm feeling he is showing that confidence. I'm really feeling he's coming around. If he came around now, that would be huge and timely."
The Marlins also are optimistic that they have caught Johnson's ailment at the right time, and that he shouldn't miss more than the 15 days.
"We're trying to be very careful here," Rodriguez said. "That's why we decided to put him on the DL for 15 days and go from there and see how he feels. They don't think it's too serious. They think it's mild inflammation -- just to rest those two weeks and he's going to be fine. It's a matter of shutting him down for two weeks."
In his most recent start, Johnson struggled getting loose and he had to battle in his five innings on the road against the Mets. It was a difficult night to pitch because the start of the game was delayed 80 minutes due to an unplayable infield after a lot of rain.
The delay altered Johnson's pregame routine, but the right-hander noted that his shoulder acted up a bit the Friday before, during his bullpen session leading into the Mets game.
"It was a tough night to pitch," he said of his no-decision vs. the Mets. "It was one of those days that it seemed nothing was going right, from the outside stuff, not the pitching. The weather, the time of the game, the feel -- everything was off. I didn't know until after the game [that his velocity was down]."
To make room on the 40-man roster for Buente, infielder Donnie Murphy was transferred to the 60-day disabled list.
"There's no good time to do [go on the DL], but this is probably the best time -- early in the season, catch it before it carries on into other starts," Johnson said.
"I'm kind of at peace with it. It took everything I had to go and say something. Once I did, it almost felt better, [like] something lifted off my shoulders. Get it right and get back to feeling good like I did at the beginning of the season."