Mafi, 29, will join Jamie Joseph's Brave Blossoms at their training base in Urayasu, near Tokyo, the Japan Rugby Football Union (JRFU) said.
Mafi was charged by New Zealand police with intent to injure following an altercation with former Melbourne Rebels team mate Lopeti Timani in July.
The incident happened after the pair had spent a night drinking with each other following a Super Rugby match against the Otago Highlanders.
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After being released by the Rebels, number eight Mafi pleaded not guilty in September and was later cleared to play for his current side Shining Arcs in Japan's Top League.
The JRFU have said they will revisit that decision if and when Mafi's legal situation changes.
The Tongan-born number eight made four appearances for Japan at the 2015 Rugby World Cup in England.
(Reporting by Jack Tarrant; Editing by Ian Ransom)
