San Francisco coach Kyle Shanahan met with Garoppolo and C.J. Beathard on Tuesday to inform them of his decision.
Garoppolo was acquired by the 49ers in a trade with the New England Patriots last month. He made his debut with his new team on Sunday in mop-up duty after Beathard left with a leg injury.
Beathard started the past five games after replacing Brian Hoyer, who began the season as San Francisco's starting quarterback.
Beathard suffered a bruised knee and strained hip Sunday, but neither was deemed serious. It is unclear whether Beathard's injuries had anything to do with Shanahan's decision.
Beathard was 22 of 38 for 201 yards and no touchdowns against the Seahawks.
On Monday, Shanahan said he would probably announce his starting quarterback on Wednesday.
"I'd like to talk to the staff. I'd like to watch some Chicago (Bears film) first," he said Monday. "We just finished up Seattle, just finished up watching the game with the quarterbacks and then came in here. I'll have a decision for you guys by Wednesday."
Shanahan said Garoppolo had learned a lot by watching Beathard and by asking questions during practice.
"He's gotten better," Shanahan said. "It's still a work in progress. It will continue to be throughout the year. Hopefully he'll be a lot more comfortable going into next year."