Tomlin, a member of the NFL's competition committee, had said on Tuesday that he did not expect to be fined.
Asked about linebacker Bud Dupree's two face mask penalties in Sunday's game, Tomlin said the calls looked legitimate, then hinted many more were not.
"But some of the other stuff, man, is a joke," Tomlin said. "We gotta get better as a National Football League. Man, these penalties are costing people games and jobs. We gotta get 'em correct. And so I'm pissed about it, to be quite honest with you. But that's all I'm gonna say on it."
The news of Tomlin's fine was first reported by USA Today Sports.
Watt's roughing the passer penalty was controversial because he tried to pull off Ryan as he attempted to tackle his lower body.
Asked if his coach standing up for penalized players is gratifying, Watt said Tomlin is "doing his job."
"It's not my job to complain about the refs because my opinion means absolutely nothing," Watt said. "I'm just going to go out and play football and control what I can control."
Tomlin had shown restraint in past weeks but hinted at frustration with officiating after a Week 3 matchup with the Tampa Bay Buccaneers that featured four roughing the passer calls among 22 total penalties.
"As somebody who appreciates the game and understands we're in the sports entertainment business, it is worrisome from the fan perspective," Tomlin said on Sept. 25. "I do worry about what it's like to watch that game at home with penalties being administered at the rate that they were."