Harper, who signed a $330 million, 13-year contract with the Phillies as a free agent, has been slumping and was down to .219 with 56 strikeouts, seven homers and 25 RBIs in 41 games.
Harper told manager Gabe Kapler there was "minimal swelling" in the knee.
"There was nothing that causes any of us any concern about putting him out there today," Kapler said.
Harper came up limping against the Milwaukee Brewers on Tuesday night on a sliding catch on a foul ball to right field in the sixth inning. Harper made an almost identical catch to end the inning. He received a standing ovation only to get booed after striking out again in the eighth.
Harper struck out twice and walked twice. He's hitless in his last 14 at-bats headed into Wednesday's game against the Brewers.
"I'm not sure a day off is going to work for me mentally or physically or anything like that," Harper said Tuesday. "I just need to keep grinding, keep trying to get through it."
Harper had said he wanted to play all 162 games for the NL East leading Phillies. Kapler said Harper was "healthy, confident and wants to play" so he kept him hitting third in the lineup.
"I don't have a tangible reason why we shouldn't play him," Kapler said. "We think he gives us our best chance to win tonight. We think he will be positively impacted by being in tonight's lineup. We'll consider it on a day-to-day basis. He and I will have those conversations."
He does lead baseball with 33 walks, has an .802 OPS and has made several game-saving plays in right for the Phillies.