“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,” Winterkorn said in a statement.
“Volkswagen needs a fresh start — also in terms of personnel. I am clearing the way for this fresh start with my resignation.”
Winterkorn said he accepted his “responsibility for the irregularities that have been found in diesel engines,” but insisted “I am not aware of any wrongdoing on my part.”
“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,” he said.
“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.”
The company’s supervisory board said later in a brief statement at the company headquarters in the northern German city of Wolfsburg that a successor would be named on Friday.
Winterkorn swiftly rose to become chief executive of the entire Volkswagen group in 2007, driving it from strength to strength and clocking up a record profit of 11 billion euros ($12 billion) and sales of 202 billion euros in 2014.
In the first half of this year, it even overtook Toyota as the world leader in terms of sales, a goal Winterkorn had only set his sights on for 2018.
Nevertheless, Winterkorn, the highest paid executive in Germany with a salary of 15 million euros, also left the group vulnerable in certain areas.
VW is over-dependent on the Chinese market, which has seen growth slow sharply recently. And the German group has failed to make any substantial inroads into the US market, where it competes with local giants such as Ford and General Motors.
