Alameda County sheriff's deputies had stopped the suspect shortly before midnight on Sunday for driving a vehicle that had been reported as stolen from a Castro Valley BART station, BART said.
Facing a felony, the suspect tried to ram into one of the deputies before fleeing the traffic stop, BART said.
Deputies pursued the suspect until the stolen vehicle reached the intersection of Grand and B streets in Hayward, BART said.
At that intersection, the suspect ran a red light and hit the BART officer's car, BART said. The police officer was proceeding on a green light when he was struck by the suspect, they said.
The BART officer was not assisting the sheriff's deputies in the car chase when he was hit, BART said.
The 38-year-old officer - whose name is being withheld at this time - was transported to a local hospital with injuries that were not considered life threatening, BART said.
The officer has been with Bay Area Rapid Transit since 2001, BART said.
The suspect was arrested by sheriff's deputies at the scene and also transported to a local hospital for treatment of injuries that were not life threatening, BART said.
Deputies recovered a firearm from the stolen car, BART said.