The incident happened around 1:30 a.m. at the intersection of Main Street and Civic Center Drive.
The officer was taken to an area hospital with non-life-threatening injuries, Santa Ana police said.
The driver of the other car was given a field sobriety test at the scene, though it is unclear if he was arrested or injured in the crash.
The intersection was shut down during the investigation and was reopened about 5 a.m., police said.
City News Service contributed to this story.