Nakajima was unmarked at the back post to finish, as Japan were rewarded for their relentless attacking after falling behind just before the interval.
Abdoulay Diaby, who is the top scorer for Belgian league leaders Club Bruges, netted a penalty in the 43rd minute to give Mali the halftime lead in front of a largely empty stadium at the home of Standard Liege.
The match, which Japan hoped would give them an indication of the style of play they can expect from Mali’s neighbours Senegal at the World Cup, kicked off at lunch time in Belgium to accommodate Japanese television.
Japan will continue their World Cup preparations at the same venue against Ukraine on Tuesday.
Japan play in Group H at the World Cup and face Senegal in Ekaterinburg on June 24. They play Poland and Colombia in their other two group fixtures.
(Reporting by Mark Gleeson; Editing by Toby Davis)
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