In a statement that's just been released, Winterkorn said that he was submitting his resignation "in the interests of the company even though I am not aware of any wrong doing on my part".
No successor has yet been named by Volkswagen. Rumours earlier this week suggested that Matthias Muller, the CEO of Porsche, was being lined up as Winterkorn successor. At the time, Volkswagen denied these reports.
Today's announcement ends Winterkorn's 34 year career at Volkswagen. In 1981 he joined Audi as a senior member of its quality assurance team. He took over group product management at Volkswagen in 1995, and became the Volkswagen brand's head of technical development in 1996.
In 2002 he assumed the title of chairman at Audi, and became its head of technical development a year later.
Winterkorn became Volkswagen Group CEO at the beginning of 2007, taking over from former BMW boss Bernd Pischetsrieder.
Earlier this year fought off a bloody internal battle to remain as the company's CEO. In the process, Winterkorn saw off Volkswagen's influential chairman Ferdinand Piech, who was forced to step down as a result.
This is the full statement from Volkswagen's now ex-CEO:
"I am shocked by the events of the past few days. Above all, I am stunned that misconduct on such a scale was possible in the Volkswagen Group.
As CEO I accept responsibility for the irregularities that have been found in diesel engines and have therefore requested the Supervisory Board to agree on terminating my function as CEO of the Volkswagen Group. I am doing this in the interests of the company even though I am not aware of any wrong doing on my part.
Volkswagen needs a fresh start — also in terms of personnel. I am clearing the way for this fresh start with my resignation.
I have always been driven by my desire to serve this company, especially our customers and employees. Volkswagen has been, is and will always be my life.
The process of clarification and transparency must continue. This is the only way to win back trust. I am convinced that the Volkswagen Group and its team will overcome this grave crisis."