Lynch later shared out that he "accidentally and unknowingly" liked the tweet.
"Never intended to [like the tweet] and remain a huge believer in Jimmy," Lynch wrote.
Garoppolo completed 26-of-35 passes for 322 yards and a touchdown but threw two costly interceptions in the loss that dropped San Francisco to 8-7 on the season.
Head coach Kyle Shanahan spoke with reporters via a conference call on Monday and was asked if Lynch addressed the situation with his quarterback.
"I don't know if he did, but no, I don't think that has to [be addressed with Garoppolo]," Shanahan responded. "I think everyone in this building knows John pretty well, and as soon as you read a tweet like that, I don't think one person who knows John thinks that he did that. They were wondering how he messed that up.
"That's why I don't have [social media] like that. I would probably do the same on accident."
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