Girardi told reporters about the move during a Zoom conference call before the Phillies played Miami Marlins in Miami.
The Phillies reinstated outfielder Roman Quinn from the 10-day injured list in a corresponding transaction. Harper's placement on the injured list is retroactive to Sunday.
Harper missed the Phillies' previous two games. He is 0 for 16 in through his last four games and is hitting .274 this season.
Girardi told reporters Sunday that there was not anything medically wrong with Harper, and that he just was given the day off. He said he chose to give Harper another day off Monday, but cited his slump, not an injury.
Girardi admitted Tuesday he knew Harper was injured and did not tell reporters because he didn't want to give the Phillies' opponents a competitive advantage.
"It cropped up Saturday," Girardi told reporters Tuesday. "After the game, he didn't say anything to me. On Sunday morning, we talked and he called and said his wrist was sore.
"I gave him the day off. I didn't want [Boston Red Sox manager] Alex Cora to know I wasn't going to use Bryce. ... I thought he would be OK Monday and he wasn't. I didn't want [Marlins manager] Don Mattingly to know. We are just going to put him on the injured list."
Girardi said Harper is bothered when he swings. The Phillies have lost five of their last six games and sit in fourth place in the National League East.
Philadelphia will face the Marlins in the third game of their series at 6:40 p.m. EDT Wednesday in Miami. They play the final game of the series at 12:10 p.m. EDT Thursday at loanDepot park.