"He died today at 23:33 (22:33 GMT)," said a spokeswoman for Vienna General Hospital, where Klestil had been in intensive care since a heart attack on Monday.
Doctors had said earlier they could do nothing but hope and pray for Klestil's survival after his heart twice stopped beating, triggering multiple organ failure.
Klestil, who had a history of lung problems, was under sedation and on artificial respiration.
He was due to step down from office on Thursday and hand over the largely ceremonial presidency to Social Democrat Heinz Fischer.
Klestil won the respect, if not the affection, of Austrians for repairing much of the damage to the country's international image caused by revelations about former president and UN Secretary-General Kurt Waldheim's role in the German army under Adolf Hitler's Third Reich.
But the career diplomat also raised the eyebrows of many when he began a relationship with a young aide, prompting his wife of 37 years to walk out on him in 1994.
Klestil, who succeeded Waldheim in 1992, was also known for the famously stony face he maintained in February 2000 when swearing in the first Austrian government to include Joerg Haider's far-right Freedom party.
Born in 1932, the youngest of five children of a Vienna tram driver, Klestil spent 18 of his 35 years as a professional diplomat in the United States.
He also served as Austrian ambassador to the United Nations and the US.
Austria's president has mostly representative functions, but his voice counts on important issues and he can influence the formation of a government.