McKillop, a backup inside linebacker who was hurt in Wednesday afternoon's practice, underwent surgery Friday morning at nearby Stanford Medical Center.
The 49ers provided no timetable for his return, if he comes back this season at all. He most likely will be placed on the season-ending injured reserve list considering the severity and healing time for the injury. Recovery for both injuries is typically six to nine months.
McKillop, a fifth-round draft pick last year out of Pittsburgh, played all 16 games as a rookie in 2009, primarily on special teams.