The match was originally scheduled to be held at the Emam Reza Stadium in Mashhad, but was moved to neutral venue by the Asian Football Confederation (AFC).
In the match held at the Sharjah Stadium, Mohammad Reza Khalatbari gave the Iranian team a lead in the 19th minute.
Saleh Taher equalized for the Bahraini club in the 35th minute.
Shahr Khodro needed an 83rd-minute winner from Amin Ghaseminejad to defeat Riffa 2-1.
Shahr Khodro will travel to Hamad bin Khalifa Stadium to take on Qatari outfit Al Sailiya in the playoff round on Tuesday.