Thaddeus Young finished with 20 points and 12 rebounds for the Nets, who have recorded two of their six victories this season against Houston. Bojan Bogdanovic scored 19 points in place of injured rookie Rondae Hollis-Jefferson.
Marcus Thornton scored a season-high 32 points for the Rockets, who fell behind by 18 points and got quiet nights from stars James Harden and Dwight Howard. Corey Brewer had 22 in extended minutes after starting forward Trevor Ariza was lost to a bruised lower back after 4 minutes.
Harden was 2 for 9 for 10 points, adding nine assists. Howard, who had 22 points and 18 rebounds Saturday in a victory over Sacramento, took just five shots and finished with 10 points and nine rebounds.
The Rockets had won three in a row and were trying to get back to .500 for the first time since they were 4-4 after a loss to Nets on Nov. 11.
That was the Nets' first victory of the season after seven losses and by adding Tuesday's win, they took a pair from the Rockets for the first time since 2001-02.
Thornton scored 17 straight Houston points in the fourth, but the Rockets couldn't get the stop they needed whenever they got really close.
Both teams committed 24 turnovers in the sloppy contest.
The Rockets came in allowing 107.3 points per game, 28th in the NBA, and for a while it appeared even the anemic Nets offense would blow past that. Brooklyn had 57 points at halftime, but then stopped getting shots and instead handed them to Houston with a number of turnovers.
The Nets opened an 18-point lead in the third quarter before Thornton had six straight points to finally get the Rockets going. They cut it to 80-72 after three, and Thornton made consecutive 3s early in the fourth and then had a steal and layup to trim it to 84-82.
Rockets: Ariza was hurt in the first quarter when he landed hard on a drive to the basket, with a loud thud. He stayed down for a couple of minutes before limping to the locker room. ... Howard celebrated his 30th birthday.
Nets: Lopez became the sixth player to make 400 starts for the Nets franchise, following Buck Williams (633), Jason Kidd (504), Kerry Kittles (455), Richard Jefferson (417) and Jason Collins (405). ... The Nets, who came in averaging an NBA-best 46.9 points per game in the paint, had 54 against Houston.
Coach Lionel Hollins estimated a 10-week absence for Hollis-Jefferson, who broke his right ankle Saturday in practice. However, the Nets said an official timetable won't be known until after surgery on Wednesday morning.
Rockets: Visit Washington on Wednesday.
Nets: Host Philadelphia on Thursday.