Babin told reporters in Philadelphia that he was fined because he hit Smith in the neck area with his helmet. Earlier Thursday, he took a shot at the NFL with a pointed post on his Twitter page.
"Attn:Guy at the NFL that decides on who and how much players get fined Stop being a puppet, if you want to protect QB's, get better linemen," he wrote.
He explained the tweet later Thursday.
"That was just meant to be sarcastic," Babin said, according to the Philadelphia Inquirer. "But my main point was the person that decides the fines -- I'm assuming they're supposed to be unbiased and make decisions for themselves according to the rules and regulations -- not let outside influences affect their decision-making. You know what they say, 'One man with courage is a majority.' "
Babin said he was fined for a play in which defensive end Trent Cole also was "high-lowed ... and you can tell that (the 49ers) game planned it. So how are they going to fine me when you see a coach and players game plan to high-low arguably our best pass rusher on our team? That's a little sickening."
Cole injured his calf Sunday and likely will miss the next three weeks, but the injury didn't occur on that play, according to the Inquirer.
Babin, who leads the NFL with seven sacks, said he will appeal the fine.
"I just get a little upset, because I guarantee you, if you were to take guys who played five years ago, 10 years ago, put them on a panel, and be like, 'All right, watch these plays, do you think these are fineable offenses?' They'd be like, 'No, they should get bonuses,' " he said, according to the Philadelphia Daily News.
Babin also said there's no consistency to the NFL's punishment system.
"Oh, I'll call that one 15, I'll call that 40," he said, according to the Inquirer. "There's no blueprint, there's no grid system to say, 'OK, this is how it works, let's plug it in.' "
Babin signed a five-year, $28 million contract with the Eagles this offseason after a Pro Bowl 2010 season in Tennessee.