The two men, whose identities were not revealed, were shot dead in their car in a carpark in the Consolat housing estate in a northern district of the city shortly after midnight. The teenager was nearby and was seriously wounded in the shooting, Nunez said.
Shootings are a regular occurrence in Marseille which is known for its high crime levels.
Six people have been shot dead in the port city since the start of the year, mostly in gangland killings.
Vowing a crackdown, Interior Minister Bernard Cazenueve in September 2015 said 6,000 weapons a year were being seized from criminal groups in Marseille, of which 1,200 were combat rifles and other weapons of war.