The incident happened just before 4:30 p.m. in the 400 block of North Magnolia Avenue, according to the El Cajon Police Department.
The suspect fled after the shooting in a white U-haul truck with an Arizona license plate but police were able to track down the vehicle to the Balboa Park area.
The suspect, later identified as 29-year-old Mohammed Abdulkareem, was taken into custody shortly after 10 p.m.
Two of the victims, a man in his 40s and a woman in her 20s, were taken to the hospital in stable condition, according to authorities.
Investigators have not released any details on a motive for the shooting.
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City News Service Inc. contributed to this report.