Wheeler felt stiffness in his pitching shoulder during Tuesday's start against the San Francisco Giants.
With Wheeler roughly 20 innings over last season's total, the Mets decided he should call it a season now rather than proceed with a start Monday in Cincinnati, and potentially one more afterward.
Wheeler's innings jump was to be capped at 30 over his 2012 total. Wheeler said no MRI or doctor's exam is needed.
Manager Terry Collins ascribed the shoulder stiffness to Wheeler pitching deeper into a season than he did in the minor leagues.
"As a matter of fact, he wanted to throw a bullpen today, and I said no," Collins said. "So he's fine."
Wheeler, 23, finished his rookie season 7-5 with a 3.42 ERA in 17 major league starts. He allowed 90 hits and walked 46 while striking out 84 in 100 innings.
Overall, Wheeler logged 168 2/3 innings between the majors and minors. Collins said he should be allowed to pitch roughly 200 innings in 2014.
The Mets were using a six-man rotation, so shutting down Wheeler simply means reverting to a conventional rotation.
Ex-Red Aaron Harang will move up a day to take Wheeler's start Monday in Cincinnati.
"With what's happened with Matt, it's not the time to take chances right now," Collins said. "... In any sport, in any game, in any athlete, fatigue leads to injuries. [Wheeler is] starting to wear down. He's the one who has been talking about how tired he has been getting anyway. But he did want to go one more time, and we said no."
Harvey plans to try rehab and a throwing program after being diagnosed with a partially torn ulnar collateral ligament, but the Mets have not ruled out Tommy John surgery becoming necessary within the next two months.
"It was a group decision," Wheeler said. "I'm 20 innings over what I had last year. It's a little stiff, so we're just being cautious."
Wheeler was acquired from San Francisco on July 28, 2011 for "rental" outfielder Carlos Beltran. The right-hander made his major league debut on June 18, tossing six scoreless innings against his hometown Atlanta Braves at Turner Field.
Wheeler limited his first team to one run in seven innings at San Francisco on July 10, and described that as one highlight of his first major league season.
"I wanted to get a job out of spring training, but I knew it was kind of a long shot," Wheeler said. "I knew I'd probably go to the minor leagues and pitch through that and do well and just get my shot up here. Once I did that, I just tried to take full advantage of it and listen to everybody with open eyes, open ears."
Wheeler said his biggest improvement came in attacking hitters.
"Once I got up here, just learning that I can go right after guys and not really give them too much credit," Wheeler said.
Said Collins: "He gave me what we certainly had hoped for when we called him up. We had heard all the stories without seeing him pitch very much. We had heard all the stories about what a great arm he had, what his upside is, and he lived up to it in every which way."
Wheeler said improving his command is the next goal.
"And also repeating my delivery," he added. "I think that's the two biggest things. And I think if I repeat my delivery, command will come along with it."