Rodon, 30, looked awkward finishing his delivery on his final two pitches to Astros right fielder Chas McCormick before manager Aaron Boone and the training staff came out to see him. He attempted a couple of warmup pitches but subsequently was pulled from the game in favor of reliever Jhony Brito.
"I felt it grab," Rodon said after the game. "It felt like a cramp, then it did it again. After that it felt fine, so it was more of a precautionary type thing."
Rodon missed the first three months of the season with a left forearm strain and has struggled since returning. He saw his ERA rise to 7.33 after giving up home runs to Jake Meyers and Yordan Alvarez on Sunday.
Rodon is in the first year of a six-year, $162 million deal he signed last winter but has made only six starts for New York and now could miss more time.
"I'm pretty frustrated," Rodon said. "This is not the way I wanted to come out here and perform. I'm pretty frustrated in how I'm performing."
The injury comes on the heels of Domingo German being placed on the restricted list to undergo treatment for alcohol abuse, while the team also is contemplating putting Luis Severino in the bullpen because of his own struggles on the mound.
"We got some key guys back in there," Boone said.
The Yankees and Astros split the four-game series as they jockey for position in the AL wild-card standings. Houston currently owns a spot while New York fell to 4½ games behind Toronto for the final wild-card berth.
Outfielder Harrison Bader was asked if he's concerned about the standings with just 50 games left in the season.
"No concern at all," he said. "If we keep playing this brand of baseball it's going to be just fine."
Having a healthy and productive Rodon in the rotation would help. The nine-year veteran was optimistic about avoiding another injured list stint.
"That's not what I'm thinking," he said. "In this moment, I feel confident I should be able to pitch."