Nedney connected from 25 yards and 30 yards in the second quarter, and booted a 51-yarder in the fourth quarter.
Alex Smith completed 13 of 21 passes for 105 yards, no touchdowns and one interception for San Francisco. Frank Gore rushed for 41 yards on 19 carries, and Brandon Moore led the defense with one sack and 14 tackles for the 49ers (3-5), who had dropped their two previous games.
Brad Johnson was 21-of-31 for 136 yards, no touchdowns and one interception for Minnesota. Chester Taylor gained 96 yards on 26 carries and made eight receptions for 45 yards, while Ryan Longwell prevented a shutout with a 21-yard field goal in the first quarter for the Vikings (4-4), who have dropped their last two games.
Minnesota out-gained San Francisco, 238-133.