Paul Pierce scored 15 points and Alan Anderson had 13 for the Nets, worn out after arriving in Toronto in the wee hours of the morning after playing two extra periods in Friday's big win over the Heat.
"Guys were definitely tired from last night, getting in late," said guard Joe Johnson, who had 11 points for the Nets.
Brooklyn dropped to 1-6 this season in the second part of games on consecutive days.
"Our guys showed mental toughness and won a slug-out game, which I don't know if we could have won a few months ago," Raptors coach Dwane Casey said. "It's a testament to our guys' mental growth and mental toughness to win a game like that."
After squandering a 10-point lead in the final minutes of the third quarter, the Nets missed six straight shots at the start of the fourth and went scoreless until Pierce made one of two from the line at 8:10.
"The last six minutes of the third was tough on us," Pierce said. "It was tough for us to execute, we turned the ball over. We were up 10 points and we had a chance to really do some damage. Maybe it was fatigue, I don't know."
Brooklyn guard Shaun Livingston, who played 51 minutes Friday, was 3 for 11 from the field against the Raptors, but said blaming fatigue was the "easy way out."
"It's always disappointing for me, as a competitor," Livingston said. "That's a game I'd like to have back."
Already without injured guard Deron Williams, the Nets gave center Mason Plumlee his first career start in place of Kevin Garnett, who got the night off after playing 36 minutes against Miami. Plumlee fouled out with six points.
While the winning streak is over, Plumlee said the Nets are feeling better about themselves.
"We do have a rhythm, we do have more confidence as a group now," he said.
Livingston agreed, but cautioned against any excess enthusiasm.
"Don't relax," he said. "I think that's the main thing. We won five games but we still haven't done anything."
The Raptors closed the third with an 18-4 run, then kept up the pressure in the fourth. Back-to-back layups by Amir Johnson and Patterson gave Toronto a 78-65 lead with 7:24 remaining.
Brooklyn responded with six straight points, but Lowry hit a 3 and Patterson made consecutive jump shots to restore the double-digit cushion, putting Toronto up 85-71 with 3:46 to go.
"It was really important with them being a divisional team and playing really well right now," Lowry said. "We needed to get this win for our confidence."
DeRozan scored eight points in the opening quarter, two of them on a breakaway slam dunk after a midcourt steal, and Lowry added six to help Toronto to a 24-18 lead.
"They're playing extremely hard, they're shooting the 3 extremely well," Nets coach Jason Kidd said. "DeRozan and Lowry are playing at a high level."
The Raptors were up 40-27 with 6:16 left in the second before Brooklyn put together a 13-4 run, including back-to-back 3-pointers by Mirza Teletovic. After a Raptors timeout, Ross hit a 3, but Pierce was fouled with less than a second remaining and made both free throws, trimming Toronto's lead to 47-42 at halftime.
The Raptors went cold to start the third, missing their first six field-goal attempts before DeRozan connected on a jumper at 6:43. Brooklyn, meanwhile, started the second half on a tear, hitting four 3s in an 18-3 run that gave the Nets a 60-50 lead.
Sparked by 11 points from DeRozan, and five consecutive missed shots by the Nets, Toronto moved in front again at the end of the third. DeRozan connected on three straight possessions, including a 3 with less than a second left, as the rejuvenated Raptors carried0 a 68-64 lead into the final period.
"A lot of things were against us tonight and we still had a chance there until the end of the third quarter," Pierce said.
Raptors F Tyler Hansbrough (left ankle) missed his fifth straight game. ... Brooklyn's next game is Thursday in London against Atlanta. ... The Nets are 5-13 on the road. ... Toronto outrebounded Brooklyn 49-39. ... The Nets have used 17 different starting lineups this season. ... Rapper Drake, who is Toronto's `global ambassador,' was honored with a Drake Night promotion. The Grammy winner announced the starting lineups, and his official DJ Future the Prince performed at halftime.