Lynch ran off the sideline and into a scrum after Chiefs cornerback Marcus Peters hit Raiders quarterback Derek Carr late, drawing a flag for a personal foul. Several Raiders offensive linemen went after Peters, an Oakland native and close friend of Lynch.
Peters showed up for the game wearing a Beast Mode sweatshirt from Lynch's apparel line.
Lynch, who had two carries for 9 yards before the ejection, bumped line judge Julian Mapp in the chest and then grabbed the official by the jersey before letting go and tending to Peters.
"I was disappointed he ran out because I knew we had a 15-yard penalty and we'd be in good shape," Raiders coach Jack Del Rio said. "I told him you can't leave the bench like that. That was about it. Next thing I knew, he was being tossed. The referee told me he had actually put his hands on him."
An NFL spokesman on Friday said the league is reviewing Lynch's actions for a fine and a possible suspension.
Physical contact with an official carries a fine of $30,387. If the NFL suspends Lynch for coming off the bench to join the altercation, it would cost him a game check of $79,411.
Lynch was seen sitting in the stands after being ejected Thursday. The NFL spokesman said that would have to be handled as a "club issue" by the Raiders.
The running back was in the locker room to congratulate his teammates after the win but didn't speak to reporters. He and Peters were spotted together on the BART (Bay Area Rapid Transit) after the game.
"I don't have any problem with Marcus coming in and hitting me. He knows that. I told him, 'I got no issue. Just play ball,'" Carr said. "Obviously, Marshawn came out and did his thing. You never want a guy to get kicked out. That stinks. But just from knowing him, I know that he was out there just taking care of us."
Raiders offensive tackle Donald Penn said he entered the fray to protect Carr and that he didn't realize at first it was Peters who had delivered the late hit.
"I ran over there and got him off of him because the refs weren't doing their job of protecting my quarterback when he's on the ground," Penn said. "It was a big old commotion. I saw Marshawn come out there."
Penn noted the relationship between Lynch and Peters, and said Lynch was just trying to protect him and get him to the sideline.
"I didn't know if they were just talking," Raiders defensive end Khalil Mack said. "I didn't know if [Lynch] was just talking trash to [Peters], trying to play around or what. Knowing that you got DC on the ground and you see a guy hit him late -- these guys love their quarterback, and they are going to protect him at all costs, but in that situation, we got to use our head."
Lynch came out of retirement this season and was traded from Seattle to the Raiders. Lynch said he wanted to make a comeback so he could give something back to his hometown of Oakland before the Raiders move to Las Vegas in 2020.
He has rushed for 266 yards and two touchdowns in seven games.
The Associated Press contributed to this report.