Coast guards originally took the vessel into custody after it was spotted off Japan’s southwestern coast.
Beijing has accepted Tokyo’s handling of the incident, describing it as a “regular fishery case”.
Similar arrests last year in disputed waters sparked a major diplomatic confrontation between the two states.
The boat with its captain and 10 crew members have been allowed to leave Japanese territory following payment of a 300,000 yen (£2,400; $3,850) fine.
The crew was originally arrested on 6 November following a chase near Japan’s Goto islands, off the coast of Nagasaki.
According to the Japanese authorities, the vessel was given multiple warnings to stop in both Japanese and Chinese and was only brought to a halt after being rammed.
In contrast to previous fishing disputes, both Japan and China have avoided allowing this case to escalate into a political confrontation.
Last year, a similar incident in disputed waters off the Senkaku islands (known as Diaoyu in China), caused a major breach in relations between the two countries.
The waters around the Goto Islands are undisputed Japanese territory