In a game of few chances at Sharjah Stadium, Tomiyasu converted a header after 20 minutes and Juan Antonio Pizzi's side failed to mount a comeback.
Pizzi had been criticised for Saudi Arabia's conservative approach during their group matches and once again they offered too little in the final third to trouble four-time winners Japan.
Hajime Moriyasu will have been pleased with Japan's clinical performance, but he will be without Newcastle United forward Yoshinori Muto against Vietname in the next round after the 26-year-old picked up his second booking of the tournament.
Japan scored from their first corner of the game, Tomiyasu taking advantage of Saudi Arabia's loose marking to rise on the edge of the six-yard box and beat goalkeeper Mohammed Al Owais to his right with an accurate header.
Saudi Arabia pushed forward and sought a response, but the closest they came to equalising before half-time was a curling Hatan Bahbri shot that flew narrowly past the post.
The game opened up after the interval and Bahbri sent an effort bouncing just wide of Shuichi Gonda's goal just after the hour mark.
But even when presented with a free header from eight yards out inside the final 20 minutes, centre-back Ali Hadi Albulayhi failed to hit the target and ultimately Japan progressed without ever looking worried at the back.