UAE had topped the group in Bishkek with nine points while Oman had seven, the same as Bahrain, but was ahead on better goal-difference. In Bishkek, Oman beat Nepal 5-0 on Wednesday and defeated the hosts 3-0. It had lost to UAE 1-5 and drew with Bahrain 1-1.
Jordan, Saudi Arabia and Qatar emerged as group winners to seal the last three automatic slots.
They join Tajikistan, UAE, Australia, South Korea, Japan, Vietnam and China who also won their respective groups.
The ten group toppers were joined by five best second-placed teams - Iraq, Thailand, North Korea, Chinese Taipei and Malaysia.
The 15 teams will join host Indonesia in the finals next October.