The host nation are the perennial underachievers of regional football and they were outplayed before a large crowd at the Tianhe Stadium, although many left early.
The writing was on the wall when Ryohei Yamazaki bundled the ball over the line after 10 minutes, with China immediately put on the back foot.
They held on till half-time before Kensuke Nagai picked up a loose ball in the penalty area and buried it in the net on 58 minutes.
China were stunned and Daisuke Suzuki put the game beyond their reach six minutes later to seal an impressive win for Japan.
It leaves the hosts with a big job ahead to qualify from Group A after Malaysia earlier beat Kyrgyzstan 2-1.
The game kicked off with Japanese and Chinese spectators separated amid a simmering diplomatic row over Japan's arrest of a Chinese trawler captain and a history of bitter rivalry between fans.
Cameras, banners and bottles containing any liquid were also banned at the match to prevent any "untoward situation", but the game passed off peacefully with only a smattering of Japanese in attendance.
The last time the two countries met, at the Asian under-19 championships in China in October, Japan's squad were booed and one spectator snatched their national flag from ceremony personnel while their anthem was played.