Jonas Valanciunas had 14 points and 13 rebounds and Tyler Hansbrough had 12 points and 11 rebounds as the Raptors won for the sixth time in seven games and completed the first season sweep of Milwaukee in franchise history.
Toronto had dropped 11 consecutive games against the Bucks coming into this season, but has since won four straight.
Ramon Sessions scored 21 points, Jeff Adrien had 19 points and Brandon Knight 18 as the Bucks lost their 14th straight road game, matching a record for futility set in the 2004-05 season.
Milwaukee has not won away from home since beating Philadelphia on Feb. 24.
The loss guaranteed that the Bucks(15-66) will finish with the worst record in the NBA. Milwaukee came in trailing Philadelphia by two games in the standings.
Knight, Milwaukee's leading scorer, returned to the lineup after sitting out Saturday's loss at Washington with a sore right hip.
The short-handed Bucks, who have five players injured and another suspended (center Larry Sanders), had just nine healthy bodies available against Toronto.
Sessions and Knight both hit 3-pointers as Milwaukee used a 12-1 run to cut its deficit to six points, 92-86, with 6:53 remaining.
That was as close as Milwaukee got, however. Vasquez made a free throw after Sessions was called for a technical, Lowry added a driving layup and Valanciunas added a pair from the free throw line, putting Toronto up 99-88 at 5:51.
Toronto's DeMar DeRozan got the night off to rest, with Vasquez taking his spot in the starting lineup. Vasquez made an impact right away, hitting three of Toronto's six 3-pointers in the first quarter, as the Raptors built a 32-19 lead after one.
Vasquez had two more 3-pointers in the second, getting eight points and four assists as Toronto took a 59-46 lead at halftime.
Lowry, who didn't score in the second, had 10 points in the third as the Raptors took an 84-79 lead into the final quarter.
NOTES: The Raptors won 47 games in the 2006-07 and 2000-01 seasons. ... DeRozan made a brief address to the crowd as the Raptors unveiled their Atlantic Division championship banner before the game. ... Toronto finished its home schedule at 26-16. The Raptors play their final regular season game at New York on Wednesday. ... The Bucks host Atlanta in their final game Wednesday. ... Brendan Shanahan, who was introduced earlier in the day as president of the Toronto Maple Leafs, watched from a courtside seat.