Brotherton, who had been in the top UK marketing post since September 2005, was previously marketing director for VW Commercial Vehicles. He replaced Gary Savage, who became head of operations.
Audi said that it was in the process of finding a replacement for Brotherton. Industry sources believe the frontrunner for the role is former Skoda head of marketing Chris Hawken, who is currently Audi's brand communications manager.
Brotherton most recently oversaw a £5m ad campaign for the A6, which broke last month. The campaign highlighted the fact that Audi had filed more patents than NASA in the development of the car to promote its emphasis on technological advancement.
Recently Audi has looked beyond traditional marketing methods. Last year it launched the Audi Channel, which broadcasts 24 hours a day on the Sky platform. The content for the channel, which is overseen by Savage, is commissioned out by its advertising agency, Bartle Bogle Hegarty.