Stanton originally announced his resignation on Aug. 8 but told university officials he would stay on until a successor was named. Late Tuesday, calling the past few months "the most difficult period of my life," he announced his immediate departure.
"Baylor will always be my school and I will do absolutely everything I can to help with the ongoing basketball investigation," Stanton said in a statement.
During Stanton's seven-year tenure, Baylor led the Big 12 Conference in graduation rates four times.
David Brooks, the school's vice president for finance and administration, will oversee the athletic department while the search continues for Stanton's replacement.
Several media outlets have reported that former men's coach Dave Bliss orchestrated a cover-up following the disappearance of forward Patrick Dennehy. The Fort Worth Star-Telegram reported last weekend that Bliss advised players to tell investigators that Dennehy paid for his tuition by selling drugs.
"I, too, have been shocked and saddened by the activities of our former men's basketball coach," Stanton said. "I feel betrayed and cannot conceive of how he could have justified his actions."
Former roommate and teammate Carlton Dotson has been charged with Dennehy's murder.