Spencer, a fifth-year pro, will be placed on injured reserve soon after undergoing surgery Wednesday to repair the ligament. He injured his knee late in the 49ers' road victory at Seattle on Sept. 14, and missed last week's victory over Detroit.
Spencer started 39 games in his first three seasons, but has been the 49ers' No. 3 cornerback since last year behind starters Walt Harris and Nate Clements. He has six interceptions in his NFL career.
Tarell Brown and Donald Strickland will compete to replace Spencer with the 49ers, who kept 12 defensive backs on their 53-man roster to start the season. Brown, a second-year pro, got his first career interception last weekend while filling in for Strickland, who also sat out with a knee injury.