Amer Deeb scored the only goal of the match at the King Abdullah International Stadium to give Iran a first loss in the campaign.
Group E is now wide open. Iran stay top with seven points from four games, Singapore have a point less, Thailand are in third with five while Jordan are on four points and back in contention.
Iran were without Spanish-based stars Javad Nekounam and Masoud Shojaei and their absence was noted.
"I congratulate Jordan for this win, but we definitely missed Shojaei and Nekounam,” said Ghotbi according to the-afc.com.
“This win will now mix everything in the group as all the teams are close.
"We want the finish top of the group and we must learn a lot from the defeat. Jordan won because they had nothing to lose and they put in a lot of effort.
"The Jordanian players produced a great performance and if they continue this way they will definitely strengthen their chances of qualifying."