Pettway suffered the injury during a 52-20 win over Arkansas two weeks ago. Malzahn said he didn't become aware of it until last week, when Auburn was on a bye.
Malzahn told reporters in Auburn that there was no specific timetable for recovery, but that Pettway would be out for "an extended period of time."
Pettway ran for a team-high 1,224 yards and seven touchdowns last season, but he has been limited by injuries this year, missing three games.
In his absence, Kerryon Johnson has emerged as the team's feature back, rushing for 723 yards and 14 touchdowns.
No. 16 Auburn (6-2) plays at Texas A&M on Saturday.