Toyama Shoji's 81st-minute goal earned Japan a place in the semifinals and also a ticket to the 2019 FIFA U17 World Cup after the teams were locked in a 1-1 stalemate at the break.
Japan will play the winner of the Australia-Indonesia quarterfinal in the last four on Thursday.
It was a spirited Oman performance and Japan had to fight hard to earn the win in a battle of former two-time champions.
Japan held the lion’s share of possession in the early minutes but hardly tested Omani goalkeeper Mitham al Ajmi.
Japan’s first clear chance came in the 14th minute, when Nishikawa Jun sent a brilliant through pass behind the Oman backline, setting up Naruoka Hikaru who had just the goalkeeper to beat but his shot to the bottom right missed the target by mere inches.
However, it was ahead just a minute later with Araki Ryotaro lobbing the ball over the Oman defenders to find a surging Jun, who beat the offside trap and forced Ajmi to parry his effort, only for sliding defender Issa al Naabi to steer it into the empty goalmouth.
Having won the title in 1996 and 2000, Oman, coached by Yaqoub al Sabahi, was undeterred by the goal and moved confidently in its search of the equaliser.
In the 21st minute, Oman threatened from the right flank and its quick exchange of passes flustered the Japanese defence, allowing Al Azhar al Balushi to send in a cross into the box and Tariq al Mashari rose highest to head the ball home.
Japan continued to dominate proceedings but Oman was solid in defence, and the match was finely poised as both teams went into the half-time break.
Yoshiro Moriyama’s charges maintained possession in the second half but were cautious moving forward as Oman looked dangerous on the counter-attack.
Jun came close to breaking the stalemate in the 54th and 59th minutes but Ajmi was on top of his game, making fine saves.
Shoji scored the winner from close range, courtesy of Jun’s impressive low cross as Japan held on for the win.
Later, a disappointed Oman coach Sabahi said, “It was a close game but in the end, football is about who takes the chance, takes the win.
“Also, Japan played better in the second half and created many chances and that’s why (it won). Maybe it’s about fitness but we were a little bit down. Sure (I am proud), we are happy, we are always willing to take the boys up higher to the next level.”