Japan moved to the top of Group B on goal difference. It and Jordan each have 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.
Japan goalkeeper Eiji Kawashima was sent off in the 70th for fouling striker Sanharib Malki.