The Niners announced Saturday that Lance had the surgery Friday to remove hardware that was causing irritation in the ankle.
Lance was injured in a Sept. 18 win against the Seattle Seahawks. He had surgery the following day to repair what the team called a "fractured fibula and ligament damage" in the ankle.
The latest surgery was the result of a lingering issue from that initial procedure, the team said in a statement.
"Due to the location of the fracture, the required hardware placement was close to a tendon in Lance's ankle," the statement read. "During the rehab process, their close proximity proved to cause irritation in his ankle. After consulting with multiple experts, the decision was made to have the hardware removed to prevent future issues in the ankle."
According to the 49ers, Lance will continue his rehab process and is expected to make a full recovery in time for organized team activities in the spring.
The 11-4 Niners are on their third starting quarterback, rookie Brock Purdy, heading into their Sunday meeting with the Las Vegas Raiders. Jimmy Garoppolo, who replaced Lance, is recovering from a broken left foot.