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 metres after good work from Yan Song.
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.
