In Match-day Three of ACL in Doha, Mehdi Taremi gave visiting team an early lead just six minutes into the match but Rodrigo Tabata equalized the match 13 minutes later.
Tabata then put his side 2-1 up in the 58th minute from the spot after Jalal Hosseini upended Sebastian Soria in the box.
Sergio Garcia scored the third goal for the host with two minutes from time.
The win sees Al Rayyan leapfrog Persepolis and Al Hilal to the top of the standings after the Saudi Arabian side drew 2-2 with Al Wahda in Tuesday’s other Group D encounter.
Esteghlal Khuzestan of Iran was also held to a 1-1 draw by Qatar’s Lekhwiya in a match held in Ahvaz on Tuesday.
Hassan Beytsaeid put the host side in front after seven minutes when he picked himself off the floor to convert from the penalty spot as Esteghlal sought to maintain its perfect start to the campaign, Tasnim reported.
But Ismaeil Mohammed found the back of the net in the 11th minute to level the scores and earn Djemal Belmadi’s team a draw that sees the Qatari side maintain the two-point gap between the teams at the top of Group B.
Debutant Esteghlal Khuzestan had already earned back-to-back 1-0 victories over Al Fateh of Saudi Arabia and the UAE’s Al Jazira.