It happened on North Portland Avenue between Park and Myrtle avenues just before 4:15 a.m.
Police say the black SUV was involved in a minor crash with a transport van when a gunman walked up to the driver's side window and opened fire.
The driver, 50, was shot in his right cheek. He was said to be awake and speaking to emergency service workers as he was rushed to NewYork-Presbyterian Brooklyn Methodist Hospital.
He is listed in stable condition.
The gunman ran away from the scene and into the nearby Walt Whitman NYCHA building.
He is described as a man with a large build, wearing a black shirt and gray shorts.
Detectives are now trying to figure out the connection between the crash and the shooting.
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