Favors' two foul shots with 41 seconds remaining put the Jazz ahead for good at 104-102 and he added another with 4 seconds left to seal the victory.
Favors finished with seven rebounds and two blocks while Al Jefferson pumped in 28 points for Utah.
The Nuggets, meanwhile, saw their four-game winning streak snapped despite 21 points and nine boards from Kenneth Faried.
Ty Lawson supplied 16 points and nine assists for Denver.
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