The Nuggets won for the second straight time without Anthony, the NBA's second-leading scorer, who sat out with a sprained left ankle. Anthony also missed five games earlier this month with a bruised knee, and Denver won three of them.
Denver held the Rockets to 18 points in the final quarter to take control. The Nuggets have won three of the last four games Anthony has missed, holding the opponents to an average of 94 points in the victories.
"Since January, we've been trying to get more serious about every game, every situation, every circumstance," Denver coach George Karl said. "Early in the season, I don't think we made as many big-time defensive plays as we made last year. Our defense is starting to play better."
Chauncey Billups scored 21 points, Nene added 18 and Denver went 29 for 39 from the free throw line to win in Houston for just the fourth time in 16 trips.
Martin has 12 double-doubles in his last 16 games, another reason why the Nuggets have surged while Anthony has been in and out of the lineup this month.
"He doesn't get enough credit," Billups said. "He's been phenomenal for us. He's more aggressive at both ends of the court."
Houston was up by two after three quarters, and led 80-79 after Brooks' free throw with 8:40 left. The Nuggets answered with a decisive 10-0 run, capped by back-to-back 3-pointers by Smith.
Houston missed 10 of its first 12 shots in the last quarter, after shooting 48 percent through the first three.
"There are stretches in the game where we play really good quarters and in two or three minutes, we throw everything out. It's been happening like that all season."
Scola scored with 4:53 left to pull the Rockets within seven, but Martin swooped in for a rebound dunk with 3:48 remaining to stretch the lead back to nine.
Brooks sank a 3-pointer with 1:18 left, and Billups was whistled for an offensive foul with 58.7 seconds to go. But Scola missed a mid-range jumper, Martin rebounded and the fans started making another early exit.
The Rockets lost for the eighth time in 12 games, despite a dominating start.
Denver mustered only 16 points in the first quarter and trailed by 15.
But Chris Andersen's free throws with 5:37 left in the half tied it at 38-all, and Billups hit two free throws on Denver's next possession to give the Nuggets their first lead.
The Nuggets went 15 for 16 from the free throw line in the second quarter, and the Rockets said that disrupted their offensive rhythm.
"We are a better team than that," Brooks said. "When we gave up 12 fouls in the second quarter, that slowed us down a lot."
The Rockets shot 49 percent in the first half (20 of 41) to lead 51-50 at the break. The Nuggets stayed close by going 21 for 24 from the free throw line.
Brooks sank two 3-pointers early in the third quarter, but then picked up his fourth foul and left the game. But the Rockets finished the quarter with a 9-2 spurt to take a 74-72 lead to the fourth. Denver went 1 for 8 from 3-point range in the third quarter.
Karl expects Anthony to return for Friday's game against Oklahoma City. ... Smith had an eventful day, making a last-minute payment to Houston attorney Rusty Hardin before the game to stall a lawsuit. Hardin was seeking unpaid legal fees after representing Smith in 2006, when Smith was accused of breaking a player's jaw in a pick-up game. Smith paid a chunk of the fees, and has 30 days to settle the debt and void the lawsuit. ... The Nuggets had only seven assists, a season low for a Houston opponent. ... Denver's 39 free throw attempts were a season high for a Rockets' opponent this season.