The 35-year-old was returning to the Olympic Village in a taxi on Friday when the vehicle crashed, leaving him with "serious head injuries" that required emergency surgery.
In a statement, the German Olympic Association (DOSB) said: "According to the doctors his head injuries are life-threatening. After determining the severity of injuries, he was transferred to a hospital with a special neurosurgical department and had emergency surgery there immediately."
A colleague, Christian Kading, was travelling with Heinze at the time of the incident and was treated for minor injuries.
The crash was the second of its kind on Friday, after a media bus carrying journalists scraped another bus earlier in the day.