In addition, the league said it will consider a forfeiture of draft choices for the Steelers because Tomlin's conduct affected a play on the field.
The $100,000 fine is tied for the second-largest reported fine ever given to an NFL coach (2007 Bill Belichick -- $500,000).
The league said Tomlin's actions -- he was standing on the white stripe that borders the playing field and took a step onto the field during Jacoby Jones' kickoff return -- should have resulted in a 15-yard unsportsmanlike conduct penalty.
"As I stated yesterday, I take full responsibility for my actions, and I apologize for causing negative attention to the Pittsburgh Steelers organization," Tomlin said in a statement. "I accept the penalty that I received. I will no longer address this issue as I am preparing for an important game this Sunday against the Miami Dolphins."
Ravens coach John Harbaugh said he respected "the process" and "everybody involved."
"We certainly respect the Steelers and Mike Tomlin completely. We never really thought for one second that there was intentionality there personally," he said.
Steelers safety Ryan Clark said the idea that the Steelers could lose draft picks in this situation was "stupid."
Asked if it was fair for the league to leave the punishment open, he said, "It's not supposed to be fair."
"Roger Goodell. When has he been fair?" he said.
Clark said he applauded how Tomlin dealt with the situation.
"He accepted responsibility for it. He understands the wrong that he did and you like a man that accepts things and is accountable for his actions," he said. "We all just want to be able to move on from it."
Although Tomlin apologized for his actions Tuesday, he continued to maintain that he had no intention of affecting Jones' return.
Tomlin on Tuesday devoted the first 20 minutes of his weekly news conference to the play in which the Jones might have scored a touchdown had he not shifted direction because Tomlin's right foot was on the field.
"I think for him it was to not run from it, to not seem like he was being standoffish about the situation, accept it as a head coach and as a man," Clark said. "I think that's the reason he answered so many questions."
On Tuesday, Tomlin struck a conciliatory tone -- and pretty much executed an about-face from his comments after the Steelers' 22-20 loss last week, when he said he was in the white stripes that separate the sideline from the field because other coaches do the same thing.
"I can't be in that space and I was, so I take full responsibility for that," Tomlin said Tuesday. "It's an inexcusable blunder on my part. I understand with my position comes the charge of preserving and protecting the integrity of the game of football, and I think probably my biggest error on Thursday night is not realizing that play jeopardized the integrity of the game from a perception standpoint."
Tomlin said he'd communicated several times with Goodell and that he spoke with the NFL commissioner Monday as well as with Ray Anderson, the league's senior vice president of football operations.
Wednesday's discipline was issued by Anderson.
Harbaugh was asked Monday whether Tomlin, who is the most recent addition to the league's competition committee, should be held to a higher standard.
"I think everybody should be held to a higher standard," Harbaugh said. "We're in the National Football League. No matter what the issue, I know every coach in this league believes that certainly. So, I'll leave it at that."
ESPN.com Steelers reporter Scott Brown and Ravens reporter Jamison Hensley contributed to this report.