Jordan joined the Blue Samurai in the last eight as they came from behind to beat Syria 2-1 in a closely fought Group B clash at the Qatar Sports Club.
The results left Japan top of the group with seven points from three matches, ahead of Jordan on goal difference, with Syria third on three and Saudi Arabia last on none.
"We wished to present you with a beautiful match but we did not manage a performance that would have redeemed our performance throughout the competition," the Saudi coach Nasser Al Johar said.
Ryoichi Maeda capped a terrible first 20 minutes for the Saudis when he beat keeper Waleed Abdullah to Yuto Nagatomo's cross.
The third goal brought about some respite for the Saudi defence as Japan eased off but after coach Alberto Zaccheroni's half-time team talk the Blue Samurai regained their composure to score twice more.
"I am very satisfied with the result we achieved tonight - we overcame the first wall to reach the next stage, we have improved throughout the competition from the first game to the second and now to the third," Zaccheroni told reporters.
"I selected young players and given chances to these young players. I am very happy with the way they are performing in the competition."
At the Qatar Sports Club, overlooked by the towering skyscrapers of Doha's glitzy downtown area, Jordan needed just a point to make the last eight for only the second time but they fell behind to a 15th minutes goal from Mohamad Al Zino.
The striker rifled home from six yards after Jordan goalkeeper Amer Shafi could only parry Sanharib Malki's low drive.
Dyab was also at fault for Jordan's second goal as he failed to deal with a long punt from goalkeeper Shafi allowing Odai Al Saify to steal in and lift an effort over the on-rushing Mosab Balhous in the 59th minute.
"We played well and we focused and concentrated and were full of disciple tactically and we achieved a good result to satisfy the fans and the Jordanian people," coach Adnam Hamed told reporters.
