A stunning 33rd minute strike from Yousef Ahmad set the twice quarter-finalists on their way, before two goals from striker Hamza Al Dardour all but ended the contest.
The two scorers were among four changes coach Ray Wilkins made to his side following the opening 1-0 loss to Iraq that leaves their hopes of making the last eight slim.
With a Group D finale against holders Japan to come, Wilkins knew a first win since being appointed in September was required at the Melbourne Rectangular Stadium.
However, his side almost made the worst possible start when Palestine midfielder Hisham Salhi cannoned a shot from over 22 metres against the crossbar.
The Jordanians enjoyed more of possession from then on but struggled to create chances in the absence of forward Ahmad Fayel, who was in a semi-coma state and suffering from hypothermia after a lengthy wait in a cold drug testing room following the Iraq defeat.
But Ahmad made the breakthrough, taking a pass from Al Dardour on the left and shifting the ball on to his right foot before precisely curling into the far corner.
Al Dardour then went from provider to goal scorer after Abdallah Deeb's brilliant step over fooled Abdallatif Al-Bahdari and gave him space but his cross shot was heading wide before his team mate helped divert it in.
Palestine pushed for a goal to bring them back into the contest but struggled to create anything clear cut and a second from Al Dardour in first half stoppage time looked to settle the match.
The forward converting a low, right wing cross by Oday Al Saify that goalkeeper Ramzi Saleh stretched for but could not reach.
(Writing by Patrick Johnston in Singapore; Editing by John O'Brien)
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