Garoppolo, 26, was sent to San Fran for the 49ers' 2018 second-round pick in a surprise move at the trade deadline by the Patriots.
Tom Brady's former understudy finally made his debut Sunday after Beathard suffered a knee contusion in the final minutes against Seattle.
He entered Sunday's game for Beathard with 1:07 remaining and connected with Louis Murphy on San Francisco's only touchdown of the game, a 10-yard throw in the corner of the end zone.
Shanahan made it clear from the start he was in no rush to shove Garoppolo into the lineup, but with each passing week, fans and pundits alike wondered what the team was waiting for.
Beathard was injured in Sunday's game against the Seattle Seahawks, which pressed Garoppolo into brief duty. "That's up to Jimmy and how it works out here and we're going to work our best to get him ready".
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Garoppolo, an Eastern Illinois product, won his first start by rallying the Patriots past the Arizona Cardinals 23-21 in the opener, throwing for 264 yards and a touchdown.
Garoppolo replaces rookie C.J. Beathard under center, who went 1-4 in five starts this season.
Beathard was 22 of 38 for 201 yards and no touchdowns against the Seahawks. It is unclear whether Beathard's injuries had anything to do with Shanahan's decision.
On Monday, Shanahan said he would probably announce his starting quarterback on Wednesday.
If he does want to become a franchise quarterback, Garoppolo will have to prove his worth in the final five games of the 49ers season.