The win took Shabab Al Ahli within one match of qualifying for the West league stage with the side to face Qatar's Al Gharafa on August 13 in the second preliminary stage.
Iran's Sepahan found a way past the tight Shabab Al Ahli defense just before the break, with Mohammad Mehdi Mohebi opening the scoring with his shot from the center of the box.
Boosted by the goal, 2007 AFC Champions League runner-up Sepahan started the second half on the front foot but it was Shabab Al Ahli who found the back of the net next, drawing level through Sardar Azmoun.
The newly-signed Iran international was on the pitch for mere seconds when he found the target, sending his shot high into the Sepahan net from the center of the box.
Neither side was able to find the target again in the remaining minutes of regulation time but that changed 11 minutes into extra-time with Yahya Al Ghassani putting Shabab Al Ahli ahead, taking advantage of Sepahan goalkeeper Payam Niazmand.
Yuri Cesar netted Shabab Al Ahli's third in the 109th minute with Al Ghassani scoring his second of the evening just before the final whistle as the UAE side moved within one match of securing a place in the group stage.