Wiggins, who scored a season-high 29 points, gave Minnesota the lead at 107-106 by knocking down a 3-pointer from the left wing with 2:05 remaining.
Towns, who scored all of his 22 points after halftime, added a top of the key 3-pointer with 1:43 left for a 110-106 edge.
Lowry recorded his most productive night of the season and posted his fourth career game with 40 points. He made 14 of 25 shots and hit six 3-pointers.
Wiggins and Towns helped Minnesota extend its home winning streak to nine games on a night when Jimmy Butler (sore right knee) and Jamal Crawford (sprained left big toe) did not play. The duo combined to make 17 of 28 from the field as Minnesota shot 46.9 percent.
DeMar DeRozan added 20 for Toronto, which shot 47 percent.
Taj Gibson added 14 points, eight rebounds and a key block of Jonas Valanciunas that preceded Towns' 3-pointer. Marcus Georges-Hunt contributed 12 and also drew a charge on DeRozan with 22 seconds left.
Minnesota led 113-108 when Georges-Hunt drew the offensive foul and the guard split a pair with 15.3 seconds left. After Serge Ibaka missed a long 3-pointer and Lowry split a pair at the line with 8.4 seconds left, Jeff Teague provided the final margin.
Before getting the late 3-pointers, Minnesota took an 87-83 lead into the fourth when Gorgui Dieng's 3-pointer banked off the glass to cap a 12-3 run.
Toronto was within 92-90 on a 19-footer by DeRozan with 9:06 left in the fourth but Minnesota responded again with a 10-2 run to get a 102-92 lead on two free throws by Wiggins with 7:10 left.
Lowry and DeRozan then combined on seven points as Toronto scored the next 11 points shortly before the late 3-pointers.
--Field Level Media
Toronto | Minnesota | |
Kyle Lowry 40 | Scoring | Andrew Wiggins 29 |
Delon Wright 6 | Assists | Jeff Teague 10 |
Delon Wright 6 | Rebounds | Karl-Anthony Towns 10 |
Kyle Lowry 6 | Free Throws Made | Karl-Anthony Towns 8 |
DeMar DeRozan 3 | Steals | Nemanja Bjelica 2 |
CJ Miles 3 | Blocks | Taj Gibson 2 |
Team | Points | FG% | 3PM-3PA | FTM-FTA | Assists | Rebounds | Blocks | Steals | Turnovers |
Toronto | 109 | 47.0 | 12-33 | 19-21 | 23 | 35 | 7 | 7 | 15 |
Minnesota | 115 | 46.9 | 7-16 | 32-42 | 21 | 44 | 3 | 4 | 11 |