Also, the NFL fined Ravens linebacker Ray Lewis for his helmet-to-helmet hit on Steelers receiver Hines Ward in the same game. Lewis wouldn't disclose the amount of the fine but a league source told ESPN NFL Insider Adam Schefter that the linebacker was docked $20,000 for the hit.
Clark was flagged for his hit on Baltimore Ravens tight end Ed Dickson late in the first half. Clark hit Dickson in stride, appearing to lead with his shoulder, but both players' helmets made contact.
"There wasn't anything malicious about it," Clark said. "It wasn't a spear. It wasn't a forearm to the head. It wasn't any of those things and to be fined $40,000 for that? To me it's either targeting me as a single player or it's targeting this team."
The Steelers have been fined 13 times for more than $182,000 this season, with Clark's latest the biggest of the bunch.
Clark's agent told the Pittsburgh Post-Gazette that his client will appeal the fine.
Clark said that coach Mike Tomlin informed him of the fine and told him the hit was used by Tomlin on Monday as an example of a good hit in the team's film review.
"I was actually expecting to get a call back and say that it wasn't wrong, because it wasn't," Clark said. "I did everything I was asked to do and (NFL commissioner Roger) Goodell and all those other guys, they sit in their office with their suits and make these decisions on what a split-second reaction by the player is and this time it's wrong."
This is the second straight week that Clark has been disciplined by the league. Clark, the team's representative to the NFL Players Association, was fined $15,000 for a hit out of bounds on New England tight end Rob Gronkowski two weeks ago.
"This time it's wrong, not that I respected Roger before this," Clark told the Post-Gazette.
Steelers linebacker James Harrison also is expected to receive a fine for a helmet-to-helmet hit in the game, a source has told Schefter.
The Steelers aren't into conspiracy theories, but they're also the only team in the league that voted against the CBA. Clark, who serves as the team's union player representative, believes NFLPA executive director DeMaurice Smith should get involved. His teammates don't think it's a bad idea.
"That's his job. I think he should do something because right now it seems like they can do whatever they want to," Harrison said.
The NFLPA did not immediately return a request for comment from The Associated Press.
Regardless, Clark argues if the hit against Dickson was against the rules, he's not sure what's legal anymore.
"Am I supposed to let him catch it and then wait for him and hug him?" Clark said. "Should I throw a pillow at him? Should I blow a whistle? 'Hey look, I'm about to tackle you.' No, that's not football."
The Ravens' Lewis agrees.
"You can't stop playing defense the way defense has always been created to play," Lewis said. "When the receiver has the ball, your job is to disengage him from the ball. You never want to hurt nobody. I've been in this business too long. I just think once you start getting into these fines I don't know how they come up with the numbers most of the time."
Neither does Clark, who threatened to go out and blatantly earn the fine next time.
"So it's going to turn into if you're going to fine me $40,000, I might as well put him to sleep for real or I might as well blow his knee out," Clark said.
Information from ESPN NFC North blogger Jamison Hensley and The Associated Press was used in this report.