Denver forward Andre Iguodala's three-point shot at the end hit nothing but net, but upon review the ball failed to leave his hand before the buzzer and the basket was waved off, leaving the Warriors with the win.
The Warriors improved to 9-6 on the year, moving back into a tie for the Pacific division lead, thanks mainly to David Lee's game high 31 points and nine rebounds.
Klay Thompson added 21 points and Stephen Curry 20 in a see-sawing contest where the Warriors led by as many as 12 but also trailed by 16 at one point.
"It was an unbelievable victory and everyone played their part," Lee said.
"We had an up and down game, it usually is between these two teams, we were double overtime last time in this building and now we have a similar game tonight so I'm just happy we came through.
"Our team top to bottom has had a will to win all season. We've had injuries, we've had distractions, but at the end of the day we came out and wanted to get victory more than the other team."
Igoudala had three free throws with three seconds left and made the first two before failing on the third but the Nuggets made the rebound.
A first attempt to gain victory failed and the ball ricocheted out of bounds, but a video review saw Denver controversially retain possession.
The final inbounds pass went to Igoudala and he flushed the long shot only to have it chalked off, dropping Denver to 8-8.