The loss sent Jordan into third place in Group B with four points behind Japan and Oman.
In another match in the group, Australia beat Iraq 2-1.
With Tuesday’s results, Japan leads the group with 10 points. Next are Oman and Australia with five points, and in fourth place Jordan with four points. Iraq tails the group with two points.
In the Jordan-Oman match in Muscat, Ahmad Kano opened scoring for the hosts in the 62nd minute.
Oman doubled its lead in 87th minute when Juma Darwish found himself all alone in front of an empty net.
Jordan pulled a goal back in the 90th, when Thaer Bawab received the ball inside the area before sending a low shot past Oman’s goalkeeper Ali Habsi, who plays in the English Premier League’s Wigan Athletic.
The match was played at Sultan Qaboos Sports Complex in Muscat.