MIAMI—During the 49ers’ run to this Super Bowl, there has been one glaring absence: Colin Kaepernick.

Seven years ago, Kaepernick took the 49ers to the Super Bowl. It was the last time San Francisco made it here. But Kaepernick has been missing from the week-long hoopla ahead of this game between the Niners and Chiefs, a period when stars past and present are typically paraded around and feted. Former quarterback Jeff Garcia and running back Frank Gore, who was once Kaepernick’s teammate with the 49ers, were among the former...