Lowry had 30 points and 11 assists, and Raptors beat the Nuggets 116-102 on Sunday night.
Williams scored 31 points as the Eastern Conference-leading Raptors completed a sweep of the season series against Denver. They also beat the Nuggets 112-107 in overtime on Dec. 8.
The Raptors, who have won seven of eight, got 10 points apiece from Lowry and Williams in a 28-point fourth quarter.
"Lou got hot and made some shots and we stuck with our principles," Lowry said. "We knew if we stayed the course and played our game we'd be all right."
Ty Lawson led Denver with 28 points, and Wilson Chandler had 20 points and 10 rebounds.
Kenneth Faried, who had 26 points and a career-best 25 rebounds in Friday's win over Minnesota, had 17 points and 19 boards for the Nuggets, who have lost three of four.
"It was frustrating in the fourth quarter," Faried said. "We couldn't score a bucket for some reason. And when we did, they had an answer for it. Lowry and Williams got really hot."
Toronto, coming off a 12-point win at the Clippers on Saturday, led by one when Williams hit two free throws and a 3-pointer to give the Raptors a 100-94 lead. After Nate Robinson missed a 3-pointer, Lowry sank two foul shots to push the lead to eight.
The lead grew to 109-98 on a three-point play by Lowry with 3:59 left. Denver never got closer than nine the rest of the way.
"When Lou gets it going you want to find him," Lowry said. "Our team's like that. We're unselfish. We want everyone to be successful."
The Nuggets were swept in the season series for the first time since 2003-04.
"Sixty-one points between Lou Williams and Lowry were too much to overcome," coach Brian Shaw said. "We didn't crowd their shooters so they rose up and they shot 3-point shots with a high comfort level. That was the difference. We had to grind out for the shots we got and they were comfortable with the shots they got."
Faried's layup midway through the third quarter gave Denver a 76-75 lead. Toronto went back up by four but a steal and layup and a jumper by Nate Robinson cut the Raptors' lead to 88-87 heading into the fourth.
Toronto's reserves played a key role in the series sweep. The Raptors' backups outscored Denver's 49-17 in the earlier win. Sunday, the margin was 53-20 for the Raptors, led by Williams' 31.
"Our bench gave us great energy. Lou gave us energy," coach Dwane Casey said. "I thought that was very important."
Raptors: Guard Landry Fields missed his fourth straight game because of a concussion. Fields has passed two of the three tests to be able to return, Casey said. "My understanding is he passed a couple parts of it," Casey said. "But there is another area that he still has to pass. And he has to do it under stress."
Nuggets: Forward Darrell Arthur played for the first time after sitting three games. He missed the first two because of a strained lower left leg and sat out the third because he hadn't taken part in a full practice coming off the injury.
Raptors: At Portland on Tuesday.
Nuggets: Host Los Angeles Lakers on Tuesday.