Three goals in five minutes virtually sealed Jordan an early victory as midfielder Ahmad Ayman Abdallah opened the scoring in the 16th minute.
Their lead was doubled by Ali Ahmad Hajabi three minutes later and Nepal were rocked again just seconds later as Abdel Qader Alalem further widened Jordan's advantage.
Nepal regrouped and held Jordan at bay for the next 22 minutes but poor defending saw them concede another two goals just before the half-time break.
Mohammad Khaled Obeidat found the back of the net in the 42nd minute and before Nepal could recover, Alalem scored his second of the match in the 43rd minute.
Alalem completed his hat-trick two minutes into the restart and Saraj Muneer Alma'aitah put the icing on an emphatic win with Jordan's seventh goal in the 80th minute.
Nepal will have a chance to bounce back when they play Kuwait on Monday while Jordan are next in action on Wednesday, when they play Sri Lanka.