Not only did the Yankees not add a starter to their rotation by Tuesday’s trade deadline, they also scratched ace Gerrit Cole from his scheduled start against the Phillies with what was termed “body fatigue.”

He was replaced by Will Warren, who made his MLB debut at Citizens Bank Park on Tuesday.

Cole said he didn’t bounce back well from his previous start against the Mets last Wednesday, when he gave up six runs.

The fatigue is not related to the elbow inflammation that sidelined Cole in spring training and prevented him from making his season debut until June 19. No tests were scheduled.

“It’s nothing really specific,’’ Cole said. “I’m a bit run down.”

Aaron Boone also noted Cole had been battling a stomach bug.

The plan is for Cole to take a few extra days before his next start, perhaps this weekend against the Blue Jays in The Bronx.

Cole went through a fairly quick ramp-up after his recovery from the elbow injury before he made his season debut in June, which may have played a role in what he’s going through now.

“You hope it’s just part of the process,’’ Boone said before acknowledging the obvious.

“He’s also not pitching today,” Boone said. “We hope it’s just fatigue.”

Cole went through his normal work between starts, but still didn’t feel right Monday, which is when the decision to bump him was made.

The right-hander told the team he still wanted to pitch, but was overruled after discussions with Boone, pitching coach Matt Blake and GM Brian Cashman, as well as the training staff.

“With what he’s been through this year, you don’t want to run him out there and put him in a bad situation,’’ Boone said.

While all sides indicated the concern level was low regarding Cole, he has yet to regain the form he had last year, when he was the unanimous winner of the AL Cy Young award.

Cole added it’s “very early” in the year for him, given his lengthy absence to start the year.

“It’s still six starts into the season for me,” Cole said. “Everyone else is in the middle of it all, so I feel different than other people.”

If the Yankees hadn’t been able to slide Warren — the team’s seventh-ranked prospect, according to MLB Pipeline — onto the roster easily and he wasn’t lined up, Cole said he might have made Tuesday’s start.

The Yankees were able to take advantage of Thursday’s off day and have another off day on Monday, which eases some pressure on the rotation.

“This is about putting more gas in the tank to be put in a position to take the ball next time and the time after that,’’ Cole said.

He had pitched well in his previous two outings before the step back against the Mets, but Cole said his velocity and stuff remained OK.