The Cardinals had to choose between the two with the return of right-hander Jake Westbrook. He had been on the disabled list since June 9 with elbow inflammation, and was activated as expected to start Friday at Miami.
Wacha, 22, made a rapid ascent after pitching last year for Texas A&M, joining the Cardinals for three starts. Lyons is three years older and has more professional experience, which was a factor in the decision, manager Mike Matheny said.
"You can't forget - Wacha was in college a year ago," Matheny said. "It's nice having that left-hander in the rotation. It has been nice to watch Tyler do his thing. He has been very efficient and given us a chance when he has been out there. Michael did a great job too, but right now it's a better fit for Tyler."
Lyons, who will start Sunday against the Marlins, is 2-2 with a 3.51 ERA in four games. Wacha went 1-0 with an ERA of 4.58.
Wacha's return to the minors will give him a chance to improve command of his fastball, Matheny said.