Chinese fans vented their fury at the final whistle after Japan scored twice in a controversial second half.
Koji Nakata had given Japan a 2-1 lead in the 65th minute with a hotly-disputed goal, the midfielder bundling in a Shunsuke Nakamura corner though replays showed he had used his hand.
Keiji Tamada added a third goal in injury time to give the scoreline a flattering look for Japan after a tension-filled match laced with political and historical overtones.
The Japanese also won the Asian Cup in 1992 and 2000.
Japan weathered an early storm from China before taking a 22nd-minute lead against the run of play following a questionable foul on Nakamura by defender Wei Xin.
Nakamura whipped in a dangerous free kick and Takashi Fukunishi headed in from close range after a knockdown from Takayuki Suzuki to silence a hostile crowd of 65,000.
But China struck back in the 37th minute, midfielder Li Ming sweeping home a superb left-foot shot from 25
Japan have been booed relentlessly at the Asian Cup and were subjected to similar treatment with their national anthem inaudible beforehand through a cacophony of booing.
The Japanese players were barracked as they celebrated but more than 6,000 security staff -- including riot police, armed troops and SWAT teams -- were on call to prevent any violence.
Chinese harbour bitter resentment over Japan's military invasion and brutal occupation of parts of the country from 1931 to 1945.
