Besides Fernandes, the airlines' Executive Director Kamarudin Meranun also stood down on Monday night, reports Efe news.
"Kamarudin Meranun and CEO Anthony Francis Fernandes, have notified the Committee that they will relinquish their executive positions within the Group, effective immediately, for a period of two months or such other period that the Company may deem fit," an AirAsia statement said.
The airline added that "as advisors, they will not have executive authority within the Group".
The announcement comes after Airbus announced last week it had reached agreements with French, British and American authorities to pay fines in connection with open investigations for suspected bribes and corruption.
However, the Malaysian anti-corruption commission said it remained in contact with British authorities to investigate the allegations.
AirAsia allegedly agreed to buy 180 Airbus planes in exchange for the aircraft manufacturer sponsoring Formula 1 racing team Caterham owned by Fernandes.
The airline denies wrongdoing and claims it has never used intermediaries to negotiate with the European manufacturer.
The British anti-fraud agency SFO (Serious Fraud Office) initiated an investigation in 2016 for the use of intermediaries by Airbus to secure civil and military contracts.
After receiving export credits from government agencies in Europe, the manufacturer was obliged to mention the intermediaries involved in its contracts to avoid criminal proceedings.
Airbus later decided to suspend the use of these consultants and launched a transparency operation to seek a negotiated exit with several countries' authorities to avoid a judicial conviction.
Fernandes and Kamarudin have denied the accusations, saying they were leaving the company to "not harm it".
( With inputs from IANS )