Trailing 1-0 with 12 minutes left, the Saudis turned the game around with goals from Naif Hazazi and Osama al-Harbi to move third in Group Two with seven points from five games and get a shot at a playoffs berth.
Masoud Shojaei's impressive 57th-minute strike looked to have been enough for Iran, but the shock defeat left them fourth in the group on six points. North Korea lead on 10, followed by South Korea, who have played one less game, on eight.
Faced with missing out on the finals for the first time in 20 years, the Saudis, under new coach Jose Peseiro, blocked out the deafening roars of the imposing Azadi stadium and attacked the Iranians from the start.
Hazazi had what appeared to be a legitimate headed goal disallowed on 36 minutes and Nassir al-Shamra had a penalty appeal waved away after being brought down in the area six minutes later.
Iran had a clear cut chance to score seven minutes after the break when Limaki Mohamma hesitated in front of goal and had his close-range effort blocked.
Mohamma turned provider five minutes later when he passed across the area to Shojaei, who fired a potent shot into the top corner to give Iran the lead.
The Saudis silenced the crowd 12 minutes from time when Hazazi latched on to a neat through ball and coolly slotted home from seven metres.
Playing without suspended striker Yasser al-Qahtani, the Saudis grabbed the winner with four minutes left when al-Harbi leapt high in the air to head home Abdoh Autef's dangerous corner.
The top two teams in the group qualify automatically, with the third placed team able to advance via two playoff matches.
