Mohammad Reza Khalatbari's 80th minute strike cancelled out Kim Jae-Sung's 10th-minute goal to give the Iranian side a 3-2 win on aggregate over the South Koreans and a first semi-final berth after their 2-1 victory in Isfahan last week.
After Kim's goal levelled the tie on aggregate, Seol Ki-hyeon blew the hottest of chances to put Pohang up in the 69th minute when he somehow sprayed a shot at an open goal from seven metres after getting past keeper Shahab Gordan.
Zobahan, who had previously never made the knockout round of the tournament, will meet Saudi Arabia's Al Hilal who reached the semi-finals despite a 4-2 defeat by hosts Al Gharafa in Doha.
Beaten 3-0 in the first leg, Al Gharafa levelled the tie with first-half goals by Mirghani Al Jain, Younus Mahmood and El Assas.
Younus scored again in extra time but Al Hilal scored twice in four minutes through Yasser Al Qahtani and Al Mahyani to progress 5-4 aggregate.
They were joined in the last four by Seongnam Ilhwa, who lost 2-0 away to Suwon Blue Wings but advanced 4-3 on aggregate after trouncing their Korean rivals 4-1 in the first leg last week.
Lee Sang-ho's second-half strike ignited Suwon's hopes of an unlikely semi-final berth after Yeom Ki-Hun found the left corner of the net with a brilliant 25-metre free kick in the 32nd minute. Seongnam then weathered a tense last half-hour.
"I feel a little uncomfortable that we progressed to the semi-final by losing," said Seongnam coach Shin Tae-yong.
"In the game, Suwon played well in all aspects. We needed the big win from the first leg to get through."
Seongnam will meet Saudi Arabia's Al Shabab who clinched a semi-final spot despite a 1-0 defeat by Jeonbuk Motors in Riyadh.
Kim Jee-wong's long-range strike after 23 minutes ignited the Korean side's hopes of overcoming a 2-0 first-leg defeat but the Al Shabab defence held firm for the remainder of the game.
