Brent Barry added 19 points as the Sonics extended their winning streak to five games. The Timberwolves had a seven-game winning streak snapped.
Seattle was eight games under .500 after losing to the Los Angeles Lakers in Allen's debut on Feb. 23, but it has bounced back to win its next five led by the dominance of its new shooting guard, who is averaging 28 points, 7.6 rebounds, and 7.5 assists since leaving Milwaukee.
Allen made 10-of-20 shots, including 4-of-7 three-pointers, and 5-of-5 free throws as the Sonics cooled off red-hot Minnesota, which had the longest winning streak in the West.
"There is nothing special to our game plan, except that we are playing hard, we are playing together, and we are having fun," Allen said. "We won't know how good we are until this season is over with."
"These guys are playing really well right now," said Seattle Coach Nate McMillan. "They've been solid the last five games, and offensively, we can find ways to score. The team is just in a real good rhythm."
The Sonics had a 60-57 lead midway through the third quarter before scoring 12 of the next 16 points. Allen opened the burst with a jumper and closed it with a 17-footer for a 72-61 edge with 2:58 left.
Minnesota pulled to within 75-71 just 2:26 into the fourth quarter, but Allen sank consecutive three-pointers to spark a 10-0 spurt as Seattle pulled away. The Sonics had their largest lead at 90-74 on a turnaround jumper by Allen with 4:01 to go.
The Timberwolves shot 53 percent over the first three quarters, but made just 5-of-18 shots in the fourth.
"We usually execute a little better down the stretch," said Minnesota's Kevin Garnett, who managed just two points in the final period. "We got away from setting picks and doing the small things. That's the reason we didn't win the game."
Kendall Gill scored five of Minnesota's 14 points in the final 12 minutes, and was the only player on the team to score until a three-pointer by Anthony Peeler with 3:45 remaining.
Rashard Lewis scored 17 points and Kevin Ollie, who came over with Allen from Milwaukee, added 11 as the Sonics extended their home winning streak to six games.
Garnett had 22 points and 11 rebounds, and Troy Hudson scored 21 points for the Timberwolves, who lost for just the second time in 15 games.
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