Star linebacker Reuben Foster was listed as questionable for Sunday's game due to a hamstring injury. He was not expected to play, Shanahan said.
On Monday morning, Foster will no longer be a member of the 49ers. He was arrested on Saturday night at the team's hotel in Tampa, Florida on suspicion of domestic violence. It was his second such incident since February 11.
49ers players woke up to the news of the arrest and the announcement that the team will be releasing Foster.
"I definitely addressed the elephant in the room when I saw them," Shanahan told reporters after the game.
The head coach said the decision to part ways with the former first-round pick, the second overall selection of the Shanahan and John Lynch era, was made almost immediately after news of the incident reached them.
"I knew what we had told Reuben, and he didn't do what we had asked him to do," Shanahan continued. "As soon as he did that, I knew the decision that was going to be made. It was just (a matter of) when.
"[The incident] happened last night around our team meeting and stuff, so none of the players knew about it. Just John and I. We talked to the owners and slept on it. They talked about it a little bit later because I had to get ready for this game. Then we did it in the morning."
While Shanahan didn't want to elaborate on the reasoning behind the prompt decision to release Foster, he said it wasn't because the team felt the second-year player was guilty of the accusation.
"This was based off other stuff," Shanahan explained. "I don't know whether that is right or wrong. We'll see what happens in the court of law. I wasn't there, but too many things have happened.
"We tried to help him out a lot. I know he has been trying too, but this was a mess up that it doesn't matter whether he did or not. It's time to move on."
Shanahan went on to explain that Foster continued to struggle to make good decisions.
"He's gotten better in that way, but it's been too much," he added. "We care about Reuben, but no one's more important than this team. The number one rule is that you've got to protect the team, and he's put us in a bad light too much."
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