But Yankees manager Aaron Boone provided a bit of optimism for his team in his postgame availability, saying there is no MRI scheduled on Cole's hamstring and that the Yankees feel like they caught on to his issue early in the process.
"Right now, he's just experiencing some tightness, so we'll kind of see where we're at," Boone said. "I know in talking to Gerrit he feels pretty optimistic about it. It's something that's popped up before with him on other pitches."
"I was sitting out there for a couple of pitches weighing the pros and cons and I just wasn't quite sure I was going to be able to get through the inning and get some treatment on it to get back out," Cole said. "So unfortunately, I just had to pull the plug."
Cole allowed three runs, two of them earned, and five hits in 3⅔ innings. He threw 70 pitches as the Blue Jays put together several lengthy at-bats against him.
Cole struck out two, tying Philadelphia's Zack Wheeler for the major league lead with 217.
The star right-hander entered Tuesday with a 14-6 record and a 2.73 ERA. He was 4-0 with a 0.73 ERA in four starts since missing time following a positive test for COVID-19. He struck out 15 in seven innings on Wednesday against the Angels.
New York remained on top of the American League wild-card race, with Boston in the No. 2 spot. But the Yankees have lost four in a row and eight of the past 10, and only a similar struggling run from the Red Sox has kept them on top.
If Cole were to keep up with his normal place in the Yankees' rotation, he would throw on Sept. 13, in a makeup game with the Twins.
The Associated Press contributed to this report.