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.
Japan will play hosts Qatar in the quarter-finals on Friday with Jordan facing Group A winners Uzbekistan.
The dismal result was the heaviest the Saudis had suffered to Japan and capped a woeful tournament after they sacked coach Jose Peseiro following their surprise opening defeat by Syria.
The Saudis have been champions three times, in 1984, 1988 and 1996 and were runners-up to Iraq in 2007 but this is a tournament they would rather forget.
"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.
DIVING HEADER
Although they could not qualify for the last eight Al Johar had called for an improved display but his side fell behind after just eight minutes as Okazaki claimed his first after good work from Yasuhito Endo.
The 24-year-old Shimizu S-Pulse forward then doubled the lead five minutes later with a diving header after a cross from Shinji Kagawa.
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.
Maeda added his second with a header from another cross in the 51st minute before Okazaki wrapped up his hat-trick ten minutes before the end after Abdullah failed to keep out his shot.
"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."
LONG PUNT
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.
Jordan came back into the game and were handed an equaliser after 30 minutes when Syrian defender Ali Dyab rose above his on-rushing goalkeeper to loft a header in to his own net after a dangerous cross from the right.
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.
Syria replaced Dyab shortly after and sent on striker Firas Al Khatib as part of a double change but they failed to create any clear cut chances as Jordan eased to victory.
"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.
