Malzahn said Cowart, a 6-foot-3, 283-pound junior, came to him "numerous times over the last couple of weeks disappointed with his playing time."
Cowart, the No. 1 overall recruit in the 2015 class, has yet to make much of an impact for the Tigers. He has had three total tackles this season through three games.
It was more bad news for the No. 15 Tigers, after Malzahn dismissed former starting quarterback Sean White from the team following an arrest over the weekend on a public intoxication charge.
Cowart, who didn't have any career starts at Auburn, had difficulty cracking the school's talented defensive line rotation the past few years. He also missed three games during the 2016 season after undergoing an emergency appendectomy.
Cowart, who began his career at defensive end before moving inside to tackle, played in every game as a freshman and saw action in 10 games as a sophomore last season.
The Tigers, who play at Missouri on Saturday, are ranked second nationally in total defense.
ESPN's Alex Scarborough and The Associated Press contributed to this report.