Mehdi Torabi gave the visiting team a lead from a set piece in the 29th minute and Senin Sebai equalized the match in the 74th minute.
Persepolis had defeated Istiklol 2-0 on October 24 in Tehran.
Persepolis will travel to Riyadh to meet Al Nassr in Group E on November 27, while Istiklol will face Al-Duhail in Doha.