A hat-trick from striker Shinji Okazaki was the centrepiece of a comfortable Japan victory that consigned traditional powerhouses Saudi Arabia to one of the most abject and humiliating defeats in their history.
Jordan, meanwhile, had to battle back from a goal down and were indebted to some generous Syrian defending as they booked a last-eight date with Group A winners Uzbekistan.
The emphatic margin of Japan's victory saw them through as Group B winners, pipping Jordan to top spot on goal difference.
Three-time champions Japan, who needed an injury-time goal to rescue a 1-1 draw with Jordan in their opening game, raced into a 3-0 lead inside 20 minutes at Doha's Al Rayyan Stadium.
Reported Stuttgart target Okazaki, a replacement for injured playmaker Keisuke Honda, broke the deadlock in the eighth minute before doubling Japan's lead five minutes later with a diving header from Shinji Kagawa's centre.
Ryoichi Maeda made it 3-0 when he flicked home Yuto Nagamoto's cross in the 19th minute and Saudi Arabia, who sacked Portuguese coach Jose Pereiro after their opening 2-1 defeat by Syria, were already dead and buried.
Maeda extended Japan's lead early in the second half before Okazaki lashed home his third in the 80th minute as the hapless Saudis, themselves three-time champions, crashed to a third successive defeat in the competition.
A draw would have been sufficient to take Jordan through at the expense of Middle East neighbours Syria and they saw Hasan Abdel Fattah fire narrowly wide after only 36 seconds at the Qatar Sports Club Stadium.
Syria gradually assumed control of the game, however, and on 15 minutes they took the lead.
Sanharib Malki's low shot was parried by Jordan goalkeeper Amer Shafi into the path of Mohamed Al Zino, who gleefully slammed the ball into an open goal from six yards.
Syria were through as things stood, but with their fans launching a premature Mexican wave, Jordan levelled.
It was a desperately poor goal to concede, defender Ali Dyab rising to meet Amer Deeb's innocuous cross from the Syrian right and succeeding only in heading the ball over goalkeeper Mosab Balhous and into his own net.
Jordan completed the turnaround shortly before the hour mark with another goal that owed much to statuesque reactions in the Syrian defence.
A goal-kick from Jordan goalkeeper Amer Shafi was allowed to reach the edge of the Syria box and striker Odai Al Shaify capitalised on the hesitancy to poke the ball past Balhous and send the Jordan fans into raptures.