Right-hander Cristhian Martinez was recalled from Double-A Jacksonville to take Sanchez's place on the roster. Sanchez's move is retroactive to June 3.
Sanchez (1-4, 5.55) came off the disabled list Tuesday and started that night's game against Milwaukee. He allowed one run and two hits in three innings of a 10-3 win against Milwaukee. It was his first start since May 7.
Gonzalez said Sanchez felt discomfort while throwing in the bullpen earlier Thursday.
"He didn't feel right, so why have him go out there and pitch without the confidence he needs," Gonzalez said after Florida's 4-3 victory over the Brewers.
Sanchez, who threw a no-hitter in September 2006, had surgery on the right shoulder in June 2007. He said the shoulder felt "tight" on Wednesday.
"They're doing the right thing. I have to be 100 percent to be on the mound," Sanchez said.