Stephen Curry, battling foul trouble much of the night, added 14 points in the first meeting between the teams since the Warriors, as the sixth seed, ousted third-seeded Denver 4-2 in the first round of the playoffs last spring.
Lee tore his right hip flexor in the fourth quarter of the first playoff game, missing the rest of the Warriors' postseason run.
"The last time I played in this building wasn't the greatest result," Lee said. "I got injured, so I wanted to come out tonight, put that behind me and attack the basket early, get any thoughts of that kind of stuff out of the way. I had some success early and I just tried to be consistent throughout the game."
Klay Thompson scored eight of his 13 points in the fourth quarter, helping Golden State overcome a fourth-quarter deficit for the fourth time this season and sending the Nuggets to their season-high fourth consecutive loss.
The Warriors also got a strong game from Andre Iguodala, a former Nugget who hit a key 3-pointer late in the game and finished with 12 points while shrugging off the constant boos from the crowd.
"It wasn't that bad," he said. "It's just our day and age in sports. There's so many transactions, and fans are so into it now with the media, being so close to the game, you see it a lot more."
For all the noise and attention over his return, it was the game that Lee put together in his first game back in Denver that made the difference for the Warriors, Iguodala said.
"He went to work for us early to get us our lead and when we hit a little bit of a drought, we went back to him and he kind of got us out of it," Iguodala said. "He's been doing a great job of wracking up those double doubles and being a go-to guy."
Ty Lawson had 16 points to lead Denver, which was outscored 25-15 in the final period. Andre Miller and Timofey Mozgov had 14 points apiece.
"We didn't have a good game," Miller said. "We haven't had a good month. We need better practices. We need to get better when we come back from Christmas. It is always frustrating when you are struggling."
Mozgov also had 11 rebounds while starting in place of injured of Kenneth Faried, who was held out of the game to rest a sprained ankle.
The Nuggets used a 10-run, capped by successive 3-pointers by Lawson and Wilson Chandler to go in front 55-52 midway through the third quarter for their first lead of the game.
Nate Robinson's stepback jumper gave Denver a 64-62 lead going into the fourth quarter, and the game remained tight throughout the period.
After Miller made one of two free throws pulling the Nuggets to within 80-78, Iguodala, a former Nugget, drained a 3-pointer to give the Warriors a five-point edge with 3:19 remaining.
Miller made a jumper for Denver with 2:24 left and the teams traded turnovers before Chandler's attempt at a game-tying 3 with 42 seconds left to play hit the rim and bounced away. The Warriors responded with a turnaround jumper by Thompson to help seal the win with 22.6 seconds remaining.
"I don't think we are playing with the confidence and the sense of urgency it takes to win," Miller said. "We have to figure out the way to get our confidence back and share the ball a little better."
The Warriors led by as many as 15 points in the first quarter but settled for a 47-43 halftime lead, getting consecutive baskets by Lee in the last minute of the second period after the Nuggets evened the score on a driving dunk by Mozgov.
Golden State had a 30-point first quarter but had barely half that in the second, when the Warriors were held to 17 points. It was their lowest scoring second quarter since being held to 13 against San Antonio on Nov. 8.
NOTES: Mozgov has three double doubles this season. ... The Warriors missed their first eight free throws of the game before Lee connected on a pair with 1:09 left in the third quarter. ... Andrew Bogut had 11 rebounds to go with his four points. It was his ninth straight game with double digit rebounds.