Japan were seemingly coasting to victory through skipper Makoto Hasebe's 35th minute goal when keeper Eiji Kawashima felled Sanharib Malki who had just been wrongly flagged for offside by the linesman after a mix-up in the Japan defence.
Japan's Italian coach Alberto Zaccheroni explained to rreporters that "the referee said the Syrian player was not offside, that our player had played the last ball back.
"He sent Kawashima off for the foul, but the linesman was wrong to flag for offside."
The Japan players reacted angrily to the decision and protested that play should have been stopped when the flag went up. However, Iranian referee Torky Mohsen ruled that the game was still active when the foul took place.
"He had a different view to the assistant," said Zaccheroni who added he was relieved to have won. "We played well, we were in control and we are still in the competition," he said.
SYRIAN SANDWICH
After Japan regained their discipline following the first seriously controversial incident of the tournament, Kawashima finally walked off and Firas Khatib fired past their substitute keeper Shusaku Nishikawa to make it 1-1 after 76 minutes.
Six minutes later Mohsen awarded Japan a penalty after Shinji Okazaki was sandwiched between defenders Belal Abduldaim and Ali Dyab.
It looked a soft decision but Keisuke Honda scored from the spot to restore Japan's lead.
In the sixth minute of stoppage-time, Syria defender Nadim Sabag had a moment of madness when he ran out of the defensive wall and hacked at the ball before Japan took a free-kick. That earned him a second yellow and he walked off shaking his head.
Syria's Romanian coach Valeriu Tita was unhappy about that incident and about conceding the decisive penalty.
"Their goalkeeper deserved the red card but we didn't deserve one," he said. "But I admit, my team started with some fear. They were scared but later on they restored their confidence after Firas came on at halftime.
"He can't play for longer as he has been injured. I am not sure it was a penalty either. The referee saw it that way though."
After playing two matches Japan and Jordan have four points with Syria on three while three-times champions Saudi Arabia were eliminated after their second defeat by Jordan earlier on Thursday.
Syria meet Jordan in their last match on Monday while Japan play the Saudis.
LATE DRAMA
With the game at the Qatar Sports Club Stadium seemingly meandering to an inevitable end, there was little indication of the drama to come with 18 minutes to play.
Japan had quickly asserted their mastery over the west Asians whose upset win over Saudi Arabia in their opening game was expected to give them more confidence going into this one.
But Japan, who had won all six previous internationals between the two countries dating back to 1978, were in
