Japan moved to the top of Group B on goals scored. It and Jordan each has four points, one more than Syria. Only the top two advance to the quarterfinals.
Midfielder Keisuke Honda scored the winner from the penalty spot in the 82nd minute after a foul on striker Shinji Okazaki.
Japan midfielder Makoto Hasebi opened the scoring off a pass from Daisuke Matsui in the 35th, but Syria striker Firas al-Khatib leveled with a penalty in the 76th after Japan goalkeeper Eiji Kawashima was sent off for bringing down striker Sanharib Malki in the box.
Japan's players fiercely protested the referee's decision to award a penalty and hand a red card to Kawashima, claiming the linesman flagged offside before the foul was called.
