Four pitches into his outing, Colon departed after getting struck by a comebacker off the bat of leadoff man Whit Merrifield.
The Mets announced Colon suffered a right thumb bruise and that X-rays were negative.
Colon whiffed at the shot with his glove hand and it struck his exposed pitching hand. Trainer Ray Ramirez raced to the mound, and Colon departed without attempting a warm-up pitch.
"The first thought that popped into my head was, 'God, please don't let this be a broken thumb,' because I just had never been hit there before," Colon said through an interpreter after the bullpen recorded 26 outs in a 2-1 win. "So I just had to pause and think about it."
Said manager Terry Collins: "When he said, 'I don't think I can throw,' Ray said, 'He's done.' And that's when I said, 'Oh, man, this thing is liable to be broken,' because he usually can pitch through a lot of injuries."
Colon next is scheduled to pitch Sunday against the Atlanta Braves. Collins said the Mets would have a better idea on Wednesday about whether Colon, despite avoiding a fracture, might require a DL trip.
The Mets scratched right-hander Logan Verrett from Tuesday's scheduled start with Triple-A Las Vegas in case they need to promote an arm.
"I think I just have to wait until tomorrow to see how it's feeling," Colon said. "I know that I grabbed a ball a little bit ago just to get an idea. I felt OK."
Said Collins: "I think we'll know more in the morning, after he's had treatment on it all night. It swelled up on him pretty fast out on the field. We'll see how he is tomorrow. If he has trouble moving it tomorrow, we'll have to certainly take a look at that."
The Mets had promoted Sean Gilmartin earlier in the day from Las Vegas with Jim Henderson landing on the disabled list, but Gilmartin was not yet available to take over for Colon because the southpaw had thrown 100 pitches in a Pacific Coast League game on Saturday. Instead, reliever Hansel Robles entered and pitched 3⅔ innings of one-run ball. The bullpen logged 8⅔ innings in all.
"That's a tremendous job they did tonight, especially for Robles," Colon said. "I know he was caught off guard with having to run out there at the spur of the moment."
Matt Harvey volunteered to pitch an inning, but Collins declined. The manager said he gave no thought to using Syndergaard once Colon was knocked out so early.
The Mets had decided to have Colon pitch on standard rest in the series opener to give Syndergaard an extra day, because Syndergaard had thrown 115 pitches in his last outing while attempting a complete game against the Pittsburgh Pirates. The decision also lines up Syndergaard to pitch Monday's series opener against the first-place Washington Nationals in D.C., rather than the previous day against the Atlanta Braves at Turner Field.
Colon had entered Tuesday's start with a 3-0 record and 1.93 ERA in his past five starts.
If his injury is significant, the Mets' heralded rotation suddenly is thin, with Verrett or Gilmartin the candidates to step in. The Mets also announced Tuesday that Zack Wheeler, who was due to begin a rehab assignment as he works back from Tommy John surgery, felt elbow discomfort and instead will be examined Wednesday at the Hospital for Special Surgery in Manhattan.