Thornton, who appealed the ban last week, was suspended for punching and injuring an unsuspecting opponent in a game at Boston on Dec. 7.
He slew-footed Penguins defenceman Brooks Orpik to the ice and landed gloved punches to his head. Orpik was knocked unconscious and suffered a concussion.
Bettman heard Thornton's appeal at a hearing in New York last Friday.
Thornton and the NHL Players' Association could still elect to appeal to a neutral arbitrator. Thornton has seven days to make that decision.
"We respect the process including the ability to attend the hearing with commissioner Bettman in support of Shawn, Bruins general manager Peter Chiarelli said Tuesday in a statement. "At this time, we will decline comment until the process is complete and Shawn has exhausted all rights available to him."
Buffalo Sabres forward Patrick Kaleta is the only player to use this appeals process under the current collective bargaining agreement, and no player has gone to the neutral arbitrator. Bettman upheld Kaleta's 10-game suspension for an illegal hit on Columbus Blue Jackets defenceman Jack Johnson.
Under terms of the CBA, Thornton will forfeit US$84,615.45. He is eligible to return Jan. 11 when the Bruins face the San Jose Sharks.