Thornton will miss the Sharks' games against the Tampa Bay Lightning on Saturday and Anaheim Ducks on Tuesday and is eligible to return Thursday against the New York Islanders. He will forfeit $77,419.36 in salary, with the money going to the Players' Emergency Assistance Fund.
Thornton had an appeal hearing with commissioner Gary Bettman at 11 a.m. ET Saturday, and the suspension was upheld, multiple sources told ESPN.com.
John Thornton, Joe's brother and agent, issued a scathing statement afterward: "The league once again failed to follow any precedent they have set when making disciplinary decisions. They stated this was most similar to the [Nick] Foligno hit [earlier this season]. which only resulted in a $2,500 fine.
"When Joe asked the league, directly, what he could have done differently, they could not clearly explain. I guess being 5'9" was Joe's only solution to avoid this suspension. We are extremely disappointed with the league's decision and feel the continuing uncertainty with league actions will only hurt the fans of the NHL."
The league, when told of John Thornton's comments, declined to comment.
Perron won't play Saturday night. Blues president John Davidson said Perron is "day to day with headaches."
Davidson also took exception to anyone thinking Joe Thornton didn't warrant the two-game suspension.
"Joe Thornton is a terrific player but he crossed the line," Davidson said. "Is he not supposed to be subject to what the penalties are in this league if he crossed the line? Joe Thornton is not a dirty player. But he crossed the line. We have a player that can't play tonight because he got a shoulder to the head that was blindsided."
On Friday, Joe Thornton said he was surprised at the two-game suspension.
"Yes, I was," he said. "I didn't actually see the hit until this morning. I didn't intend to hurt or do anything bad to him. He kind of ran into me, to be honest with you. Last night and this morning I had about three dozen text messages from players around the league saying they can't believe I even got a penalty."
Sharks general manager Doug Wilson, in a statement, said: "We strongly disagree with the two-game suspension handed down by the NHL today to Joe Thornton. What is most distressing is that we feel the suspension is not consistent to the recent reviews by the league following similar collisions resulting in players leaving the penalty box and establishing their place on the ice, including [Los Angeles Kings defenseman] Willie Mitchell on [Chicago Blackhawks forward] Jonathan Toews."
Thornton got a five-minute major and game misconduct for an illegal hit to the head in the second period of the Sharks' 2-0 loss at St. Louis on Thursday.'p>
Thornton was coming out of the box after getting his first penalty of the season, a boarding call, when he hit Perron and got the major.
"So 11 games into the year and I get my first penalty, I was on pace to win the Lady Byng and all of sudden I get flagged for an illegal head check," Thornton told ESPN.com. "That's a little strange since I have no history with that. But it is what it is. You look at the new rule, I think they're still in limbo at the rule in itself and they're not quite sure maybe on how it should fly and I got caught in the middle of it."
After the hit, Perron returned to score his team's second goal.
"I asked the guys who hit me actually, because I didn't know who it was," Perron said afterward. "Obviously, Joe's not a dirty player. It's good I got to score a goal and it was a big one for us."
Said Wilson: "In Joe's case, it was clearly not a predatory-type hit with an intent to injure, shown by the fact that the player returned to the ice for his next shift so it is clear that the contact to the head was minimal. We put a lot of time and effort into helping define the NHL's new rule on headshots but we feel strongly that this suspension is not a reflection of the rule's true intent."
NHL disciplinarian Colin Campbell, who was in transit, did not take part in the hearing Friday. Mike Murphy, the NHL's vice president of hockey operations, conducted the hearing and decided on the suspension.
Pierre LeBrun covers the NHL for ESPN.com.