The crash happened just before 3:30 Sunday morning at the intersection of Linden Boulevard and Rockaway Avenue in Brownsville.
The MTA said the car ran a red light and struck the left side front of the bus.
The impact of the crash sent the bus careening up onto the sidewalk.
Authorities say the three people injured in the car were all taken to Brookdale Hospital.
Family members of the passengers involved rushed to the scene where they consoled each other.
The bus operator was treated for minor injuries and released.
Two passengers who had been on the bus refused medical attention.
The MTA said it was cooperating with the police regarding the investigation.
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