The 38-year-old missed a 38-yard field goal attempt against the Atlanta Falcons on Sunday, his 14th miss of the season.
The 49ers head coach told reporters: "The decision's been made, David Akers is our kicker."
Akers faced competition for his place on the roster earlier this month, when Harbaugh signed free agent Billy Cundiff, but the former Washington Redskins kicker lost out to Akers in practice and was cut from the team last week.
Akers's opposite number in the Super Bowl, Justin Tucker, has just three misses all year.
The 49ers face the Baltimore Ravens on February 3.