Thompson had last week appealed against the suspension, which was imposed after he knocked Pittsburgh Penguins defenseman Brooks Orpik to the ground before punching him during a Dec. 7 game.
"Commissioner Gary Bettman today upheld the 15-game suspension that was assessed ... by the Department of Player Safety for punching and injuring an unsuspecting opponent," the NHL said in a statement.
Bettman, who heard Thornton's appeal at a hearing in New York on Dec. 20, said the ban had been "supported by clear and convincing evidence and is therefore affirmed".
Under the terms of the collective bargaining agreement, Thornton will be fined $84,615, which is more than seven percent of his 2013 salary of $1.1 million.
Thornton's actions resulted in Orpik sustaining a concussion, the Bruins forward having pulled the unsuspecting Orpik to the ice before punching him several times in the head.
Canadian Thornton was assessed a match penalty, ejected and immediately suspended.
"This cannot be described as a hockey play that went bad, nor do we consider this a spontaneous reaction to an incident that just occurred," the NHL said in a video link posted on its website when it initially announced the suspension.
"Rather, it is our view that this was an act of retribution for an incident that occurred earlier in the game. The result of this action by Thornton was a serious injury to Orpik."
Media reports after the game said Thornton was angry because Orpik's hit to Bruins forward Loui Eriksson during the first shift knocked the Boston forward out of the game.
"I feel awful," Thornton told reporters after the game. "It wasn't my intention for that outcome. I know Brooksie. I've gotten to know him over the last seven years here ... It's not what I wanted to see or what anybody wanted to see."
- Sports & Recreation
- Ice Hockey
- Brooks Orpik
- Gary Bettman