Thornton now can appeal to an independent arbitrator and has seven days to make that decision.
Thornton had appealed the league's original decision and met with Bettman on Friday in New York. Thornton received a match penalty for attacking the Pittsburgh Penguins' Brooks Orpik during a stoppage in play at 11:06 of the first period on Dec. 7 at TD Garden.
Orpik suffered a concussion and was taken off the ice on a stretcher after Thornton slew-footed him and punched him twice in the head. Thornton had his in-person disciplinary hearing with the NHL's department of player safety on Dec. 13, and vice president of player safety Brendan Shanahan handed down his decision the following day.
Thornton appealed that decision on Dec. 17 before meeting with Bettman on Friday.
Bettman in his statement said: "I find that there is clear and convincing evidence to support Mr. Shanahan's conclusion that a suspension of 15 games is appropriate."
Bettman said he believes Thornton was looking for retribution for Orpik's earlier hit on Bruins teammate Loui Eriksson, who suffered a concussion.
"There is no question that the conduct was improper, intentional and involved the use of excessive and unnecessary force," Bettman wrote.
"Simply put, this was a bad act with a bad result, and neither will be tolerated in our game. Again, I note that Mr. Thornton has a reputation for being a 'good actor' and a model NHL citizen, but that does not eliminate the need for him to be punished appropriately for his bad act in this case," the commissioner wrote.
Thornton, who will forfeit $84,615.45 in salary, will be eligible to return on Jan. 11 against the San Jose Sharks.
"We respect the process, including the ability to attend the hearing with commissioner Bettman in support of Shawn," Bruins general manager Peter Chiarelli said in a statement. "At this time, we will decline comment until the process is complete and Shawn has exhausted all rights available to him."
ESPN.com's Pierre LeBrun contributed to this report.