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. He scrambled for four yards, converted a fourth-down pass to Aldrick Robinson and threw a 10-yard touchdown pass to Louis Murphy after rolling left.
Jimmy Garoppolo's first start with his new team will come against his hometown team.
Garoppolo against Seattle replaced rookie C.J. Beathard, who was making his fifth start after displacing veteran Brian Hoyer for the top job Week 6 in Washington.
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. He backed up Tom Brady in New England before getting traded to San Francisco.
Beathard's 69.2 passer rating ranks 34th among qualified quarterbacks.
Garoppolo said after Sunday's 24-13 loss that he was "pretty excited" about the prospect of playing in Soldier Field for the first time since entering the NFL.
After the game, Shanahan said Garoppolo's three snaps, including his impressive touchdown throw, wouldn't factor in his decision. With Beathard dealing with a knee bruise and hip strain, Shanahan likely felt compelled to go with the only fully healthy option, Garoppolo.
"To give those guys the best chance to be successful, you want to give them all the reps, which still isn't enough reps", Shanahan said Monday.