Nene scored 19 points and had 11 rebounds, Chauncey Billups added 19 points and 10 assists, and the Nuggets' defense shut down Roy to beat the Trail Blazers 97-89 on Monday night.
Roy scored a career-high 52 points against Phoenix on Thursday, but Denver's defense held the Portland guard to just eight points.
"It was a lot of everything," Roy said. "It was getting into foul trouble and, really, it was just their night."
Roy was saddled with foul trouble all game. He picked up two in the first 5:48 of the game and two more in the third. The Nuggets harassed him, having multiple guys guard him and double teaming him when he had the ball.
"Give him two," said Nuggets coach George Karl in explaining the game plan. "Whenever he touches it give him two players. Foul trouble helped us, too."
With Roy struggling, LaMarcus Aldridge pitched in with 20 points and Travis Outlaw had 15. Greg Oden, who also was in foul trouble most of the game, fouled out with 10 points.
"To be successful against a player like him, it has to be a team effort," Billups said of Roy. "Dahntay (Jones) started off great on him, J.R. (Smith) had some good minutes on him, so it was a team effort."
Anthony sat out with what the Nuggets called a right elbow contusion, which has bothered him since training camp. He will also miss Tuesday's game in Portland and Friday's home game against Philadelphia.
Without their leading scorer the Nuggets spread out the offense. Five players scored in double figures, and four had at least 15 points.
"That's the way it has to be," said Kenyon Martin, who led the Nuggets with 12 rebounds. "There are some guys who have to step up and play well, which they did tonight."
Even without Roy's offense, Portland kept it close until Denver pulled away late. The Nuggets led 85-83 halfway through the fourth when they took control. Linas Kleiza, who finished with 17 points, hit a 3-pointer and Smith's two jumpers extended the lead to 92-85 with 4:18 left.
"His 3 was huge," Karl said of Kleiza. "Great pass. We actually made some great passes and Chauncey missed some 3s, which surprised me. Chauncey's shots were daggers, too, but LK's was a big dagger."
The Trail Blazers cut it to 93-89 with 1:20 to play, but Kleiza's dunk with 48 seconds left sealed the victory.
Smith, who started in place of Anthony, finished with 15 points.
"I thought they were the more aggressive team," Portland coach Nate McMillan said. "Tonight for whatever reason we didn't attack the basket and move the ball and do the things we're capable of doing. We can play much better than that."
Roy, who hit 14 of 27 field goals against the Suns, picked up his fourth foul midway through the third quarter and left the game having scored just six points on 2-for-6 shooting. Oden picked up his fourth foul 1:13 into the second half and sat out until there was 9:52 left in the game. He fouled out with 1:31 left and the Nuggets ahead 93-87.
"I really couldn't get into a groove" Oden said. "It's hard to get into a groove when you get called for fouls and have to be taken out."
With those two out, Aldridge scored 10 points and Joel Pryzbilla scored seven points in the third to help the Trail Blazers take a 72-70 lead. The Nuggets grabbed the lead back when Kleiza hit a buzzer-beating 3-pointer to give them a 78-75 lead heading into the fourth.
Roy played almost the entire fourth quarter but was just 1-for-5 from the field.
"We had a tough time scoring when he was out of the ballgame," McMillan said. "We can't sit and wait for him to put up big numbers. There will be nights when other guys have to step up."
The Nuggets are 2-1 without Anthony this year. He was suspended for the first two games of the season. ... Portland has shot at least 40 percent from behind the arc in 12 of its last 19 games.