The last year finalist created many chances but their players failed to capitalize on most of their chances.
Jalal Hosseini scored the only goal of the match for Persepolis five minutes before halftime.
Persepolis will meet Al-Rayyan of the Qatar and Goa from India on April 17 and 20.
In another Group E match, Al-Rayyan was held to a goalless draw against Goa.