The team said there is no structural damage to his throwing arm. He will take anti-inflammatory medication and resume throwing when the discomfort subsides.
DeGrom is expected to miss Tuesday's start at Cincinnati.
"Honestly, I wasn't really that worried about it," deGrom said. "It got a little stiff last night. I thought I'd be all right. When we did a precautionary MRI, it showed a little inflammation. But I think that might be from having bad mechanics -- my arm is dragging, and it just caused it to flare up a little bit. It's nothing bad. Something flared up in there, and I think they want to be safe with it and not risk anything. It's comforting that we did get a look at it and there's nothing wrong."
Asked if he is certain he will pitch again this season, deGrom replied: "I'm pretty certain I'll be back out there."
Manager Terry Collins nevertheless said he was concerned.
"I actually called the trainer two times today trying to get a report when they were at the doctor," Collins said. "That's about as pins and needles as I can get. I needed to know, because I didn't like the sound of it last night. I didn't like what I heard. We're very lucky that it's nothing more than what it is."
During Thursday's start against the visiting Miami Marlins, deGrom motioned for trainer Ray Ramirez as he departed the game and headed to the clubhouse.
DeGrom acknowledged to media after the outing he "did not feel great" but insisted he was OK and seemed to spin the comment as though he were referring to his mechanics.
DeGrom allowed three runs on six hits and a season-high-matching four walks in the five-inning, 102-pitch outing against Miami -- a 6-4 Mets loss.
He had allowed 13 runs and 25 hits in 9 2/3 innings over his previous two outings. That had prompted Collins, suspecting fatigue, to skip deGrom's turn Monday.
Collins had initially planned to slot deGrom back into the rotation Friday against the Washington Nationals, but he was moved up a day to face the Marlins when Steven Matz had continued difficulty with a rotator-cuff impingement, and the Mets aborted having the southpaw return from the disabled list.
DeGrom has allowed 40 baserunners and recorded 44 outs in his past three starts.
Despite hanging in the National League wild-card race, the Mets have been decimated by injuries. Second baseman Neil Walker on Thursday became the latest Met to be lost for the season when he committed to having surgery to repair a herniated disk in his lower back that had deprived him of the feeling in a toe.
In an unforeseen development, considering how pitching-blessed they were to open the season, the Mets already are using rookies Seth Lugo and Robert Gsellman in the rotation. Any absence for deGrom could prompt them also to consider Gabriel Ynoa, Rafael Montero or Logan Verrett.
Montero had a spot start for deGrom on Monday against the Marlins and tossed five scoreless innings, although Montero also walked six batters and threw 100 pitches.
The only healthy established starting pitchers available are Noah Syndergaard and Bartolo Colon. In addition to Matz's shoulder woes, Matt Harvey underwent season-ending surgery in July to address thoracic outlet syndrome. And Zack Wheeler is no longer expected back in 2016 after his latest setback in his rehab from Tommy John surgery. Wheeler was diagnosed two weeks ago with a flexor muscle strain. Even Syndergaard is pitching with a bone spur in his elbow, although the Mets have suggested it will not need to be surgically removed.
Matz is due to resume throwing on Monday at the Mets' complex in Port St. Lucie, Florida.