Lou Williams added 19 points and Amir Johnson scored 17 for the Raptors, who tied a season high with their sixth straight victory.
John Wall, battling migraines and a sprained right ankle, was a game-time decision for Washington. He started and led all scorers with 28 points and had 12 assists. Bradley Beal added 26 points.
Lowry scored seven points in overtime for Toronto, which squandered a 17-point, second-half lead Friday night before outlasting the Nets.
With a win before a sellout crowd at the Verizon Center, Washington (31-17) could have pulled into a tie with Toronto (33-15) for second place in the Eastern Conference.
The Wizards trailed by as many as 21 points in the third, and 96-78 early in the fourth before Wall (10 points) sparked the rally. Washington tied it with 25.9 seconds left on a 3-pointer by Paul Pierce (19 points).
After Pierce's two free throws gave Washington its first lead of the night, 111-110 with 4:04 left in overtime, the Raptors scored six straight points, four by Lowry.
Wall's basket cut the lead to three, but Lowry drove, was fouled and hit both free throws with 1:25 to go.
DeMar DeRozan had 15 points and 10 rebounds for the Raptors, while Washington's Kris Humphries finished with 10 points and 14 rebounds.
Toronto led 33-30 after making seven of eight 3-pointers in the first quarter.
The Raptors' long-range success continued, and consecutive 3s by Greivis Vasquez, Williams and Patrick Patterson keyed a 14-0 run to start the second quarter.
Lowry's runner gave Toronto its biggest lead of the half, 53-33, with 7:01 left, nearly a minute before the Wizards managed their first field goal of the quarter.
The Raptors finished the half 11 of 18 (61.1 per cent) from beyond the 3-point line and shot 57.1 per cent (24 of 42) overall.
Raptors: Forward James Johnson missed his second straight game since injuring his right hamstring Friday. Coach Dwane Casey said Johnson had an MRI on Saturday, with the results pending. . The Raptors improved to 8-4 in the second game of back-to-backs.
Wizards: Nene was in the starting lineup after missing Wednesday's loss at Phoenix with a sore right foot. . Those attending Saturday night's game received Marcin Gortat action figures, complete with a cape but minus Gortat's Mohawk. ... Pierce is two points shy of tying Alex English for 15th place on the NBA's career list.
The Raptors host Milwaukee on Monday.
The Wizards host Charlotte on Monday.