The Japanese dominated possession and created numerous chances but the West Asians secured a memorable win thanks to some resolute defending and efficient finishing against a side who had thrashed them 6-0 at home in June.
It was Jordan's first win over Japan and put them firmly in contention to qualify for a debut World Cup after a game which was supposed to see the Asian champions celebrate another finals appearance.
While the result only delays an almost inevitable 2014 finals berth for Japan, the display highlighted Alberto Zaccheroni's need for a prolific striker able to take his chances in tough spots, while holes were again apparent in a rarely tested defence.
Japan top Group B in Asia with 13 points from six matches, with Jordan now occupying the second qualifying position after moving on to seven points from six games.
Australia and Oman, who drew 2-2 earlier in Sydney, both have six points with the Socceroos having played a game less.
The Sydney draw meant that Japan only required a point against Jordan, ranked 90th by FIFA, to reach a fifth consecutive World Cup and there seemed little doubt they would achieve that after a bright opening.
The intricate passing of the Japanese was bamboozling the Jordanian defence but Ryoichi Maeda was guilty of failing to make their dominance count.
A strong header by the forward was well palmed away in the 15th minute before a mistimed effort came off his shoulder and hit the crossbar eight minutes later after he had done well to beat the offside trap.
Jordan held firm and they made the most of one of their few attacks to grab a shock lead just before half-time when Khalil Bani Ateyah beat Shinji Okazaki to head home Amer Deeb's inswinging corner and leave the King Abdullah Stadium rocking.
More chances came and went for the visitors in the second period with Okazaki going close before Jordan, who beat Australia 2-1 at home in September, extended the advantage thanks to a brilliant solo effort by Ahmad Ibrahim in the 60th minute.
The forward collected the ball near halfway before outpacing Maya Yoshida down the right and cutting into the penalty area and tucking a left foot shot underneath Eiji Kawashima in the Japan goal.
The hosts then made one of their few errors of the game when Shinji Kagawa was allowed to stride through to collect a lobbed ball over the defence to smash home in the 69th minute and cut the deficit.
The precious points looked to have been lost a minute later when substitute Abdallah Salim gave away a penalty by desperately lunging at a through-ball that he was never going to get, only succeeding in bringing down full-back Atsuto Uchida.
However, goalkeeper Amer Sabbah came to the rescue, expertly leaping to his left to push behind the penalty from Japan's most capped player Yasuhito Endo.
Zaccheroni threw on tall forward Mike Havenaar in search of the equaliser but the Jordanians battled bravely to deny the Blue Samurai.
The emotions for the home players were too much at the fina
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