Warriors coach Mark Jackson praised his team for sharing the ball.
"More importantly we defended," he said. "That's a tough team to defend, but we did the job across the board. On the offensive end, guys came up big, especially our bench."
The Nuggets remained eighth in the Western Conference playoff race and will host the Warriors on Monday.
"The idea is we need to string some games together simply for our playoff position and hopes," Nuggets guard Arron Afflalo said.
Afflalo scored 13 of his 16 points in the first quarter and Denver had a 27-26 lead at the buzzer.
But the Warriors got 22 points from their bench in the second quarter and shot 56 percent to take a 56-49 lead at halftime.
Thompson scored nine points in the third quarter and Golden State went ahead by as many as 17 before Denver trimmed the margin to 76-68 with a 9-0 run.
The Warriors carried an 85-75 lead into the fourth and expanded it to 90-79 on Dominic McGuire's jumper two minutes in. Later, they went ahead by 12 on Lee's layup midway through and pushed the advantage to as high as 18 twice down the stretch.
The Warriors won the previous meeting between the teams this season, 109-101, on Feb. 9 in Denver...The Warriors were coming off 1-3 road trip that ended in a 104-98 loss at Utah on Friday night.
For more on the W's, head over to Golden State of Mind.