It followed the former regional powerhouse's humiliating 5-0 defeat by Japan on Monday, which left them bottom of their group with three straight defeats and out of the tournament.
It was only the second time in Asian Cup history that Saudi Arabia have not made it to the knockout stage.
The recriminations had already started with their Portuguese coach Jose Peseiro fired after their opening match loss to Syria.
When they crashed 1-0 to Jordan in their second game, King Abdullah removed Prince Sultan Bin Fahd as president of the Saudi Football Federation. His deputy, Prince Nawaf Bin Faisal, replaced him.
"The Saudi Soccer Federation has accepted the resignation of Fahd Al-Misaibeeh, manager of the Saudi national team, and his crew, and relieved Nasser Al-Johar of his post as the current team's coach," SPA said, citing a statement from Prince Nawaf.
"We vow to immediately replace them by a highly-qualified international crew and domestic aides."