Stefan Knirsch had held the position for barely ten months, replacing another top engineer who left after being suspended as part of an inquiry into the emissions cheating saga.
Audi said Knirsch was "leaving in agreement with the supervisory board" but did not elaborate on his reason for quitting.
The unexpected departure comes after Bild am Sonntag newspaper last week reported that an internal investigation by US law firm Jones Day had found that Knirsch knew that Audi's 3.0-liter diesel engines were equipped with cheating software before the scandal erupted.
He is also reportedly suspected of having made false declarations about his knowledge of the matter.
Volkswagen was plunged into crisis last September when it admitted to installing "defeat devices" in 11 million diesel vehicles worldwide.
The sophisticated software could detect when the cars were undergoing regulatory tests and lower their emissions accordingly to make them seem less polluting than they were.
Most of the 'dieselgate' cars fall under the VW brand, but vehicles made by the group's Audi, Skoda and Seat brands were also among those carrying the software.
Audi declined to comment further when contacted by AFP.
The company did not say in its statement who would replace Knirsch.
The VW group, which has announced a mass recall to repair the affected vehicles, has had to set aside billions to cover costs and fines over the scandal.
Its share price remains more than 20 percent lower than it was before the crisis broke.
On Monday, VW shares closed 2.6 percent lower in Frankfurt, underperforming the DAX 30 index which fell by 2.3 percent.