Thornton, the Bruins' captain before being traded to the Sharks on Nov. 30, received a game misconduct with 5:13 gone for his hit that drove Gill's right side into the boards in the corner to the left of Boston's net, knocking Gill out of the game.
Hitting from behind is an automatic game misconduct.
Gill said he suffered a pinched nerve in his left shoulder and wasn't upset with Thornton, one of his close friends. He also thought the game misconduct penalty was too harsh.
"It's just unfortunate that I was kind of caught in an awkward position because normally the way I would take that hit, it wouldn't have exposed itself to be a penalty," said Gill, who braced for the check.
Gill fell to the ice, lifted his left arm toward his right shoulder and rolled over before getting up. He went directly to Boston's locker room. He and Thornton, the top pick in the NHL draft in 1997, had been teammates since the 1997-98 season.
The Bruins said Gill suffered an upper body injury and would not return to the game.
The 6-foot-4, 223-pound Thornton was just behind the 6-7, 250-pound Gill when they chased the puck into the corner. Thornton actually hit Gill on his left side then stepped over him and was assessed a five-minute major penalty and a game misconduct by referee Chris Rooney.
The crowd's reaction was subdued.
Thornton had at least 80 penalty minutes in each of his last six full seasons with Boston and had 36 in his previous 39 games this season.
He leads the NHL in assists and was fourth in scoring entering the game. At the time of the trade, when both teams were struggling, he was 11th in total points. In return for Thornton, the Bruins, seeking to improve their defense, acquired defenseman Brad Stuart and forwards Marco Sturm and Wayne Primeau.
Thornton said at the time that he was "blindsided" by the trade.
At a Sharks practice Monday, Thornton said that he "loved" playing in Boston.
"I have a lot of great memories here and made a lot of friends," said Thornton, who was 18 when he joined the Bruins, "and, really, this is where I grew up and I still come back. It's a good place to grow up. I had a lot of fun as a kid and now I'm a man."
But he understood why the trade was made.
"The big thing is when teams don't go the way they're supposed to go, people get traded or people get fired. It's just the nature of the business," he said.
At the time of the deal, the Bruins had lost nine of their previous 10 games, while the Sharks were in an 0-7-3 slump. Both were in last place in their divisions. Boston won its first two games after the trade and San Jose won its first six.
Thornton had 26 points in 15 games for the Sharks before Tuesday's game after scoring 33 in 23 games for the Bruins. Sturm entered the game with seven goals and six assists in 15 games with Boston after scoring six goals and 16 points in 23 games with San Jose.