Hunter gained 26 yards on nine carries while Frank Gore chipped in with 42 yards on 17 runs for the 49ers (2-1).
Cincinnati (1-2) was led by rookie Andy Dalton, who managed 17-for-32 passing efficiency for 157 yards and two interceptions in the loss.
The Bengals got 64 rushing yards on 17 carries from Cedric Benson.
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