The attackers targeted his car in the Kamenge district reportedly with machine guns and rocket launchers.
Burundi has been racked by unrest since April, when Mr Nkurunziza announced he would seek a third term in office.
Opponents argued this contravened the constitution and there was a failed coup attempt in May.
A presidential election was then held last month which Mr Nkurunziza won, but which was boycotted by the opposition.
Gen Nshimirimana was reportedly in charge of the president's personal security and had been central in cracking down on protests.
Witnesses to the attack said four men in military fatigues had sprayed the car with bullets.
Other witnesses said rockets were also fired.
Presidential adviser Willy Nyamitwe told Reuters: "He has been killed by a bullet... He was in the car with some bodyguards but I don't know exactly what happened."
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