Gore's score tied him for the most in 49ers' franchise history with Joe Perry and Roger Craig as NFC West-leading San Francisco (9-3-1) rebounded from a loss last week to St. Louis.
San Francisco's Colin Kaepernick went 18-of-23 for 185 passing yards and scored on a late 50-yard touchdown run.
The Dolphins (5-8) dropped their fifth game in six outings as Ryan Tannehill was limited to 17-of-33 efficiency for 150 yards and a touchdown.
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