Arkansas State trailed 31-20 early in the fourth before Tres Houston caught a 38-yard catch in the end zone to start the comeback.
On South Alabama's next offensive play, Cody Brown intercepted Cody Clements' pass under pressure and Johnston White capped a 43-yard drive with a short touchdown run to give Arkansas State its first lead since early in the second quarter. Three plays later, Stone recovered a fumble in the end zone and, four plays later, Clifton returned an interception 37 yards.
Fredi Knighten passed for two touchdowns for Arkansas State (3-3, 2-0 Sun Belt) after missing three games with a groin injury.
Clements threw for 273 yards with three touchdowns and three interceptions for South Alabama (3-3, 1-1).