"We got carved up in the second half," Carlisle said. "Our effort wasn't where it needed to be. I thought we tried hard in the second half and the results were still not good."
Darren Collison had 21 points and O.J. Mayo added 18 for the Mavericks, who lost at home for the first time in four games.
Pekovic went 8 of 13 from the floor. Kirilenko and Alexey Shved each had 16 points for Minnesota.
Even with all the injuries, the Timberwolves (5-2) are off to their best start since 2001-02.
"Pretty gutsy performance by us," Minnesota guard Luke Ridnour said. "Everyone that came on the court for us just contributed."
Minnesota led by six at halftime and pushed its advantage to 64-51 on Kirilenko's dunk with 3:52 left in the third. Pekovic went down to the floor just more than a minute later and was helped off the court by a trainer.
Dallas was within 76-68 in the fourth when Carlisle was ejected. The coach stormed toward halfcourt after a shooting foul was called on Mayo, and official Jason Phillips quickly gave Carlisle consecutive technicals.
The Timberwolves went on a 9-4 run over the next 1:37, capped by Shved's 3-pointers that gave Minnesota an 85-72 lead.
Dallas cut its deficit to 85-78, but Minnesota went 5 of 6 on free throws in the final minute to put the game away.
"It's not the end of the world," Mayo said. "But at the same time, we have to get back to getting better."
Ridnour had 15 points and eight assists, and reserve Dante Cunningham chipped in 14 points for the Timberwolves.
The Timberwolves capitalized on Dallas' offensive struggles as Cunningham broke free for an easy dunk, putting Minnesota up 29-17 early in the second.
The Mavericks cut into Minnesota's lead late in the first half. They hit their final three shots to get within 45-39 at halftime.
NOTES: Dallas All-Star forward Dirk Nowitzki said during an in-game television interview that his rehab from right knee surgery is going slower than he expected. He offered no timeframe for his return. Nowitzki is about halfway through the expected six-week recovery process. ... Minnesota won for only the fourth time in its last 23 games against the Mavericks.