The Bobcats streak was stopped two losses short of the NBA record held by the 1993-94 Dallas Mavericks.
"I saw the clock," Henderson said. "I kind of grabbed the ball with about five seconds. I knew I had some time. I just threw it up there and it went in. It feels great to end that streak."
Kemba Walker led Charlotte with 25 points and Ramon Sessions finished with 23 as the Bobcats won at home for the first time since Nov. 21. Henderson finished with 15 points.
Luke Ridnour had a season-high 22 points, seven rebounds and seven assists to lead Minnesota, which has lost nine of 10.
Henderson's game-winner capped a frantic final 29 seconds after Ricky Rubio put the Timberwolves up 101-99 with a reverse layup.
The Bobcats were struggling to get a shot off before the 24-second shot clock expired.
At one point Henderson drove the lane and lost control of the ball, and Michael Kidd-Gilchrist had to save it from going out of bounds by throwing it back in. Walker tried to set up again, but the ball bounced off J.J. Barea's knee and into the backcourt.
With time running down, Walker retrieved the ball and passed it to Henderson, who pump-faked to avoid a leaping Andrei Kirilenko and then gathered himself briefly to swish the 3-pointer.
"Man, I didn't think he had time to get it off," Walker said. "He pump-faked. I didn't know if it was going in or not but he really took his time and he had a chance to gather himself. He shot it with confidence and it went in."
The Timberwolves had a chance to win the game but Barea failed to get a shot off as time expired and wound up on the floor. Acting Timberwolves coach Terry Porter and Berea argued the call with officials at midcourt, pleading that Berea was fouled by Walker as he attempted the shot.
"There was some contact there and they didn't think there was enough to call a foul," Porter said. "Four seconds is plenty of time to get an opportunity to get it off."
Porter called Henderson's game-winner after a frantic battle for the ball "just one of those fluke things."
"They were scrambling for the ball. We were scrambling for the ball," Porter said. "We had two guys on (Walker) and he found a passing lane to get it to Henderson and in a low clock situation had to turn and shoot and he made it. That's just one of those things."
Despite playing without two starters and six players overall, the Timberwolves jumped out to a 29-11 lead less than nine minutes into the game. Ridnour hit a pair of 3-pointers and Greg Stiemsma gave the Bobcats fits inside, three times getting free for uncontested alley-oop dunks.
Stiemsma had 10 points and six rebounds in the first eight minutes but struggled to produce after that, finishing with 11 points and seven rebounds.
Looking to generate something offensively, Charlotte coach Mike Dunlap went with a small lineup that included the 6-foot-5 Henderson at power forward. The Bobcats managed to cut the lead to 11 at the break and then to four at the end of the third quarter.
Charlotte opened the fourth quarter with a flurry, going on an 18-6 run as Walker and Sessions began to take charge.
"I was thinking to put the guys on the floor that are playing well and I didn't care if they were 5-foot-nothing," Dunlap said. "I just said let's find five that can make that push."
The Bobcats tied the game at 79 after a Minnesota turnover and a Walker steal led to a pair of fastbreak layups for Sessions. Walker gave the Bobcats their first lead of the game on a pull-up jumper from 18 feet with just over 10 minutes to play.
Charlotte increased its lead to eight, but the Timberwolves battled back to tie the game behind back-to-back 3-pointers from Ridnour and Berea.
Barea finished with 19 points and Rubio had a season-high 14 points and eight assists.
The 18-point deficit was the largest the Bobcats have overcome this season.
NOTES: Bismack Biyombo had his third double-double of the season for the Bobcats, finishing with 10 points and 13 rebounds. ... The Bobcats shot a season high 50.7 percent from the field. ... Charlotte outrebounded Minnesota 38-30.