The Real Madrid left-back lashed a sensational effort from just outside the box into the top-left corner with his weaker right foot as Tite's side made it back-to-back triumphs having finished their World Cup qualifying campaign with one win in three.
It was Neymar who opened the scoring in Lille, though, converting a penalty after referee Benoit Bastien made use of the VAR system. However, he failed to double his tally when Eiji Kawashima saved his second spot-kick of the match.
Marcelo ensured the Japan goalkeeper's celebrations were short-lived with a thumping strike, before Gabriel Jesus continued the strong start to his burgeoning international career with his eighth goal in 12 caps.
Maya Yoshida hit the woodwork before Jesus struck, but Japan - who left out star trio Keisuke Honda, Shinji Kagawa and Shinji Okazaki - pulled one back when Tomoaki Makino headed past substitute keeper and debutant Cassio.
There was to be no comeback, though, as Tite's men saw out the victory in routine fashion and now face a trip to Wembley to test themselves against England on Tuesday.
After Giuliano and Jesus made early breaks into the box, Brazil were awarded a penalty by referee Bastien following a VAR review.
Replays showed Yoshida hauling Fernandinho down in the box and Neymar took full advantage, sliding the ball into the bottom-right corner after a stuttering run-up sent Kawashima the wrong way.
The referee pointed to the spot again after Hotaru Yamaguchi sent Jesus to ground. Neymar switched corners and Kawashima guessed right this time to turn the forward's attempt around the post.
However, Japan could only clear the resultant corner as far as Marcelo, who sent a thunderous strike with his unfavoured right foot flying into the roof of the net from 20 yards.
Brazil were in cruise control but received a warning when Yoshida curled a free-kick, awarded for Casemiro's foul on Genki Haraguchi, from just outside the left side of the box against the join of the post and crossbar.
The Selecao took heed and extended their lead nine minute before half-time, Jesus turning Danilo's low cross home at the back post at the end of the rapid counter-attack.
Haraguchi was booked for simulation by Bastien early in the second half, while Neymar was shown a yellow card after the use of video technology for catching Hiroki Sakai with his arm.
Tite sent Cassio on for the second half but he was unable to maintain the clean sheet as Makino climbed above Jemerson to head Yosuke Ideguchi's corner into the net in the 63rd minute.
The likes of Taison, Diego Souza and Douglas Costa were awarded opportunities by the Brazil boss, but the substitutions interrupted the flow of the match.
Japan thought they had set up a tense finale when Kenyu Sugimoto headed Takashi Inui's free-kick past Cassio with two minutes remaining but the goal was ruled out for offside, and they were fortunate not to lose 4-1 as Alex Sandro nodded Danilo's delivery wide at the back post in stoppage time.