Holt caught 10 passes for 160 yards.
The Rams (6-6) won for just the second time in their last six games.
Bulger was sacked by Bryant Young late in the first quarter and was taken for X-rays, which came back negative. He was diagnosed with a shoulder sprain.
Todd Peterson kicked two field goals to account for San Francisco's only points. The 49ers are now 1-11.