The Miami native and former University of Miami star had been looking forward to facing the Dolphins for months, but he didn't participate in practice this week.
DeShaun Foster will replace Gore as the 49ers' starting tailback.
The 49ers had also signed running back Thomas Clayton from the practice squad to the active roster on Saturday.
Clayton has spent both of his NFL seasons on the 49ers' practice squad after the club drafted him in the sixth round out of Kansas State. He performed well in the preseason twice but couldn't win a spot on San Francisco's roster.
Information from ESPN.com's John Clayton and The Associated Press was used in this report.