Manager Jerry Manuel said Monday left-hander Ken Takahashi will replace the struggling Perez in the rotation.
Takahashi made his major league debut on Saturday at Philadelphia and worked 2 2/3 scoreless innings, allowing only one hit. He had his contract purchased from Triple-A Buffalo on April 27.
Manuel said the 40-year-old Takahashi will "definitely" make more than one start as Perez works in relief as a situational left-hander.
"He'll be in the bullpen until we can try to rebuild him, get him right," Manuel said, adding it won't be easy to find the right situations for Perez.
"This will be quite a challenge for us," Manuel said before Monday night's 6-4 win against the Atlanta Braves. "This will be quite a challenge for him.
"It's something that I've done before with starters. You now try to find a spot where you can get him to get some confidence."
Manuel said Perez could hasten his return to the rotation "if he's lights out" in his first relief appearance.
Takahashi's first scheduled start is Friday in New York against Pittsburgh.
Manuel said Perez was not asked to accept a minor league assignment.
Perez is 1-2 with a 9.97 ERA only months after agreeing to a $36 million, three-year contract. He lasted only 2 1/3 innings against Philadelphia on Saturday, giving up four runs and five hits.
Perez declined to speak with reporters after batting practice.
"He's taking it as a challenge," Manuel said. "I think he is not very happy with the way he's been performing. It's discouraging for him. He is one of those guys who has a lot of energy, that people like being around. ... And his teammates love him. They want him to do good. They really pull for a guy like this."
Manuel said team doctors found tendinitis in Perez's right knee, but general manager Omar Minaya said "it wasn't something that we felt at the time was a DL-able situation."
"This is the course of action we're going to take right now," Minaya said of the decision to have Perez pitch out of the bullpen.
"Jerry and I talked about it and we said, 'Let's get him in the pen first and see how things go from there.' I feel pretty good that Ollie's going to turn it around."
Perez and Manuel spoke in a closed-door meeting before Sunday's game against the Phillies was rained out.