Jordan were denied in stoppage time after coming so close to pulling off a major shock.
Jordan took a surprise lead on the stroke of half-time, sending the crowd into raptures. Hasan Abdel Fattah jinked inside Yasuhito Endo before unleashing a left-footed shot, which looked to be heading straight into the arms of goalkeeper Elji Kawashima. However, it took a wicked deflection off Maya Yoshida and ended up in the back of the net, sparking rapturous celebrations among the Jordanian contingent in the stands.
However, Yoshida would make amends in the second minute of stoppage time when he rose highest to powerfully head Makoto Hasebe's cross home at the back post. It was a crushing blow for Al Nashama who succumbled to the sustained pressure piled on by the Japanese at the end.
The opening goal had come after Japan had dominated the opening period with 71 percent of the possession. The pressure almost told after 25 minutes when a sweetly struck volley from Makoto Hasebe was beaten away by Amer Shafi to Yoshida but the defender was ruled offside.
Despite their lack of possession, Jordan had their moments in attack. Abdel Fattah had a low shot saved by Kawashima after the Japanese defence struggled with a long-ball forward on the half-hour and Basem Fathi headed wide from a back post corner on 38 minutes.
Japan cut the Jordanian defence to ribbons two minutes later with some incisive attacking play and despite a good save from Shafi, Shinji Kagawa will feel he should have scored having ghosted into the penalty box.
Four minutes into the second half, Jordan came close to doubling their lead against a lethargic Japanese defence but Odai Al Saify's header glanced narrowly wide of the goal. Keisuke Honda then stung the palms of Shafi with a powerful free-kick from the right on 55 minutes.
Alberto Zaccheroni's introduction of new Stuttgart signing Shinji Okazaki almost paid instant dividends. His cross found skipper Hasebe, whose effort flashed the wrong side of the post on 63 minutes before Okazaki himself came close to scoring six minutes later.
Both teams return to action on Thursday with Japan taking on Syria and Jordan facing Saudi Arabia.
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