USC Athletic Director Pat Haden said Cruz knowingly violated rules that limit the time athletes can spend on the practice field and participating in organized team activities.
"Adhering to all NCAA rules is paramount for each one of our coaches, student-athletes and staff members," Haden said. "Those who knowingly break NCAA rules are subject to termination."
Cruz was suspended Feb. 7 pending an athletic department probe.
Named to replace him was associate head Coach Dan Hubbs, who before joining USC last season had spent 12 years as the pitching coach at California.
Cruz had compiled a 48-63 record while guiding the Trojans.