It was the fourth win in a row for the Raptors (15-7) while the Suns (9-17) finished a six-game road trip at 2-4.
The Raptors entered the fourth quarter leading by 18 points.
The margin reached 19 before a Suns surge cut the lead to 10 on a 3-pointer by Jared Dudley with 8:44 to play.
Lowry pushed Toronto's lead to 14 when he made a 3-pointer with 5:18 left.
DeMar DeRozan finished with 20 points, eight assists and seven rebounds for Toronto. Serge Ibaka chipped in with 19 points, OG Anunoby had 16 points, C.J. Miles had 15 points and Jakob Poeltl and Fred VanVleet each had 13.
Devin Booker, who scored a season-best 46 points Monday in the victory over the Philadelphia 76ers, had 19 points, five rebounds and eight assists against the Raptors.
Alex Len added 14 points and seven rebounds, and Troy Daniels and Josh Jackson each contributed 13 points for the Suns. Greg Monroe scored 11 points and grabbed 10 rebounds, and Dudley scored 12.
Suns forward TJ Warren was assessed two technical fouls with 7:58 to play in the third quarter to earn ejection from the game. He had 11 points and one rebound in 23 minutes.
The Raptors led by as many as 17 points before finishing the first quarter with a 36-23 lead with Lowry scoring 13. The Suns had seven turnovers in the quarter and the Raptors had none.
The Raptors led 55-46 at halftime. The Suns had a 23-19 advantage in the quarter, ending a string of 12 straight games in which the Raptors had outscored the opposition in the second quarter. Toronto made seven turnovers in the quarter and Phoenix had three.
Two free throws by DeRozan had the lead at 17 with 4:23 left in the third. The Raptors led 97-79 after the third quarter.
NOTES: Suns C Tyson Chandler (rest) did not play Tuesday after recording seven points and 12 rebounds in a season-high 37 minutes Monday during a win over the Philadelphia 76ers. Greg Monroe started at center Tuesday and Alex Len was backup. ... Suns interim coach Jay Triano became the first Canadian to be an NBA head coach when he led the Raptors from 2008-2011. ... The Raptors will start a four-game trip Friday against the Memphis Grizzlies. ... The Suns will host the Washington Wizards on Thursday.