The king ordered an investigation, with the decision based on a report submitted by the kingdom's Oversight and Anti-Corruption Authority, better known as Nazaha, the Saudi Press Agency reported.
Mr Al Youbi is accused of exploiting his office for personal gain, embezzling university funds, money laundering and forgery, the royal order said.
Nazaha has been asked to “complete the necessary legal procedures against” Mr Al Youbi, the order read on Thursday.
The authority has the mandate to fight all forms of administrative and financial corruption.
Meanwhile, Times Higher Education released its latest 'World University Rankings 2023 by Subject', with King Abdulaziz University in 63rd place after climbing from the 126-150 band in which it featured in the previous rankings.
In the field of physical sciences, it was in 47th position — a big improvement from its ranking of 90 last year.
More of the kingdom's engineering institutions have made it on to the list world's top 300 universities, with seven universities featured this year, up from four in the previous ranking.