كتب : Amro Hassan
The hosts took an early lead thanks to a spot-kick from Abdou Otaif before Emirates drew level through Mohamed Al-Shehhi in the 39th minute.
Ismail Matar scored a second for UAE one minute before half-time with a brilliant volley from 30 yards out.
In the 71st minute, Saudi Arabia equalized when Faris Jumaa scored against his own net.
Ittihad Jeddah striker Nayef Hazzazi scored the Saudi's winner from an 84th minute header.
The win lifts Saudi Arabia to second in Group A of the Asian qualifications, level with North Korea on ten points.
The two teams are one point behind group leaders South Korea, who beat their Northern neighbours 1-0 earlier on Wednesday.
Saudi first goal
First goal for UAE
Ismail Matar's striker (1-2)
Saudi Arabia's leveller
Saudi Arabia's winner (3-2)