Neymar rifled in the opening goal in only the third minute but frustration grew from the Brasilia crowd before Paulinho fired in the second early in the second half and Jo wrapped it up with almost the last kick of the game.
Barcelona's new signing would exit in the 74th minute after receiving treatment on his back, but the points were already secured.
This was the first international match to use goalline technology, but it was not required to confirm Neymar's strike as he smashed the ball home from the edge of the area with only his second touch after Fred chested down Marcelo's arrowed pass from the left wing.
But if the fans hoped that heralded the start of a rout they would be disappointed with the rest of the first half, with a reminder of the pressure Brazil will be under both in this tournament and at next year's World Cup coming with the restless murmuring which began to seep from the stands.
It was not for lack of trying on the pitch as Brazil continued to look dangerous coming forward. Hulk's low cross from the right almost led to an own goal, with Japan goalkeeper Eiji Kawashima making a fine block after the ball struck his own man, while a glorious deep ball from Dani Alves just eluded Fred at the far post.
Another chance came with a quick counter-attack as Fred brought down Neymar's ball and forced a fine save from Kawashima, who was then up in time to keep the rebound away from the advancing Neymar.
There had been early warning signs at the other end too, Julio Cesar fumbling twice from Keisuke Honda and also being grateful to see the CSKA Moscow man blaze over from close range, but Brazil were doing most of the running.
Just as they had in the first half, Brazil struck early in the second, with only two minutes played when Paulinho expertly turned and then lashed an unstoppable shot at goal, with Kawashima getting to it but only able to slow, not stop, its progress towards the net.
Japan responded well, heading quickly to the other end where Shinji Okazaki poked a shot wide but Brazil gradually regained control of the match.
Fred saw half-hearted penalty appeals turned away when he tumbled on the edge of the area but there was far greater concern in the 69th minute when Neymar went down after a challenge with Makoto Hasebe and was carried off on a stretcher.
There was a thumbs-up from the physio and a brief return to action, but he continued to hold his lower back and was soon replaced by Lucas Moura.
With Hulk and Fred soon replaced, Brazil seemed content to shut up shop for the final 10 minutes but there was a final flourish when Oscar slipped the ball through for Jo to side-foot under the goalkeeper.