The move is retroactive to May 31, so Gonzalez could return as soon as next week.
Gonzalez was scheduled to start Saturday against Oakland, but manager Buck Showalter decided against it.
"He's improved, but the problem is he hasn't picked up a ball," Showalter said. "We can't take the chance of him going out there and then in the first inning having a problem with it."
Showalter said Gonzalez would throw on the side Friday and again early next week. Gonzalez would have a rehabilitative start in the minors before returning between June 15th and 17th.
Gonzalez is 3-4 with a 4.17 ERA in 11 games, including 10 starts. The discomfort in his right side became more intense after his last outing, when he pitched into the seventh inning on May 30 against Houston.
Right-hander Kevin Gausman will start for Gonzalez on Saturday. The plan is for Gausman to be recalled from Triple-A Norfolk before that game.
In other moves Friday, the Orioles recalled right-handed reliever Tim Berry from Double-A Bowie and selected the contract of reliever Evan Meek from Norfolk.
The 23-year-old Berry has never pitched in the majors. He was 3-3 with a 4.12 ERA in 11 starts with Bowie. Selected in the 50th round of the 2009 amateur draft, Berry would be the lowest-drafted player in club history to play in the majors with the Orioles -- if he got in the game Friday.
Showalter said Berry would be sent back to Bowie after Friday's game to make room for Gausman.