Russia returned to the podium for the first time since 2000 to take silver. A devastated Chinese team held their heads in their hands after they had to settle for bronze in the Rio Olympic Arena.
World champions Japan had been leading Russia by just 0.208 going into their final floor rotation with China third at 0.739.
But world floor champion Kenso Shirai set Japan on their way with a soaring 16.133. Six-time world all-around champion Uchimura then sealed the only title missing from his collection.
Japan, who reclaim the title they last won in 2004, scored 274.094 after the six rotations with Russia on 271.453 and China 271.122.
It completed reigning Olympic all-around champion Uchimura's medal collection after taking team silver with Japan in 2008 and 2012.
Britain finished two points off bronze, in fourth ahead of the United States, Brazil, Germany and Ukraine respectively in the eight-team final.