Bahrain coach Juan Anotnio Pizzi had been looking to heal old wounds after his Saudi Arabia team lost to Japan at the same stage in 2019 but Hajime Moriyasu's side put in a commanding performance and rarely looked troubled against the Gulf nation.
Japan will face the winner of the final last-16 tie between Iran and Syria later on Wednesday.
"All Asian teams here at the Asian Cup are getting better, the level of football has grown. But even though other teams are growing, we've managed to improve as well which is down to our players' efforts," Moriyasu told reporters.
"But I don't think today's performances were 100% and we can still improve."
Japan took the lead in the 31st minute when Seiya Maikuma unleashed a venomous strike that crashed off the post but midfielder Doan was alert to pounce on the rebound to score from close range.
Japan went 2-0 up just after halftime through a stroke of good fortune when an unmarked Kubo received the ball inside the box, turned and fired home, with the goal being awarded after a VAR check for an offside call.
Bahrain halved the deficit from a corner when Japan keeper Zion Suzuki saved Sayed Baqer's header but as he attempted to catch the ball when it looped up in the air, Ueda tried to head it clear and they collided as the ball went over the line.
NO CLEAN SHEET
While Moriyasu was not too concerned about their own goal, Japan have failed to keep a clean sheet in every game at the tournament so far.
"It's true we conceded a goal, every opponent we come up against will analyse us and expose our weak points," Japan skipper Wataru Endo said.
"I know we have to make this right, we have to concentrate for 90 minutes."
However, Ueda made amends for the own goal when he made it 3-1 after quickly evading three Bahrain defenders and as they tried to stop him racing away by pulling his shirt, the striker pulled the trigger from a tight angle to beat the keeper.
The game also saw Kaoru Mitoma make his return from injury and the Brighton & Hove Albion winger sent a buzz around the arena when he made several chances with his agility and speed on the ball, skipping past defenders with sublime ease.
But Japan did not capitalise on his forays into the box while Bahrain keeper Ebrahim Lutfalla also stood firm to deny the east Asian side a fourth goal.
"It was a difficult match, they were stronger, they were better than us technically and physically. They have players with great individual skills," Pizzi said.
"Japan have had the same coach for many years. Even their substitutes had the same quality when they came off the bench."
