The Saudis relied on their thrusting, rapier counter-attacks to surprise the Japanese who dominated the ball without often threatening to turn possession into goals.
Livewire forward Malek Maaz netted a brace with strike partner Yasser Al Qahtani also scoring to set up a final against Iraq, who had earlier beaten South Korea 4-3 on penalties in Kuala Lumpur.
The first half hour contained nothing more than some gentle Japanese probbing with Saudi Arabia content to sit back and hope for a moment of inspiration from their talented front pairing of Maaz and Al Qahtani.
The game got the goal it desperately needed on 35 minutes. Adulrahman Al Qahtani won a free-kick on the left after somewhat typically throwing himself theatrically to the ground.
Taisir Al Jassam rose highest to meet his cross and the ball dropped kindly to Yasser Al Qahtani who needed no second invitation to rifle home.
That seemed to wake up the Japanese who were level just two minutes later.
Centre-back Yuji Nakazawa ran unchecked from deep onto Yasuhito Endo's corner and headed powerfully home from six yards, without even a hint of a Saudi challenge.
The second period was not allowed to settle into a pedestrian affair as the Saudis broke the deadlock two minutes after the restart.
Taisir Al Jassam released Ahmed Al Bahri down the right and his pinpoint cross was headed home by Maaz at the near post.
Once again it took a goal to awake the Japanese and they drew level again after another six minutes.
Nachiro Takahara rose highest to head back Endo's corner for Yuki Abe to volley home acrobatically.
As with the first half Japan dominated the ball but the Saudis were always dangerous on the break.
And on 57 minutes they went in front again through a brilliant individual strike from Maaz, who twisted and turned two defenders before finishing with the outside of his boot.
Substitute Ahmed Al Mousa had a chance to finish the game on 64 minutes but greedily opted to shoot when a pass was needed.
Another substitute Naotake Hanyu almost took the tie into extra-time but thudded the bar from 25 yards with nine minutes to play.