"MRI was better than anticipated," Shanahan told reporters on Monday. "We'll see him when he comes in Wednesday to have an idea whether he can practice, be limited, or what his status will be."
Witherspoon was injured during the fourth quarter of Sunday's 26-16 victory over the Houston Texans at NRG Stadium. The injury occurred on the play that saw rookie safety Adrian Colbert force a fumble out of the arms of Texans wide receiver DeAndre Hopkins.
Witherspoon has started the 49ers' last six games. His first start came on October 29 against the Philadelphia Eagles, just two days before the 49ers traded away former starting cornerback Rashard Robinson to the New York Jets.
Fellow starting cornerback Dontae Johnson struggled against the Texans and allowed nine catches on 10 targets for 140 yards and a touchdown before getting benched. He also committed three penalties in the game. Johnson briefly returned to the game following Witherspoon's injury.
Witherspoon (6-3, 198) was selected out of Colorado in the third round of April's draft.