Garoppolo completed just 7 of 17 passes for 77 yards and threw two interceptions in the 43-17 setback at Levi's Stadium in Santa Clara, Calif. C.J. Beathard took over at quarterback for the second half and completed 9 of 18 passes for 94 yards and a score.
"This is a team that's very resilient," Fitzpatrick told reporters. "I think we showed that today coming out to the west coast and playing like we did, but it didn't surprise us at all.
"I think this is what was expected for us and I'm happy with the way we played on both sides of the ball."
The Dolphins forced three turnovers and had five sacks in the victory. Garoppolo missed the 49ers previous two games due to a high-ankle sprain before his return on Sunday.
"You could tell he was affected by his ankle," 49ers coach Kyle Shanahan said.
"I know he doesn't normally throw the ball that way.
"I think he was struggling a little bit because of it and the way the game was going I wasn't going to keep putting him in those positions and knowing we were going to have to throw it a lot to comeback."
The 49ers went three-and-out on the first drive of the game before the Dolphins responded with a six-play, 70-yard touchdown drive and Fitzpatrick throwing a three-yard touchdown toss to Adam Shaheen.
Dolphins running back Myles Gaskin ran in for a one-yard rushing touchdown for a 14-0 lead with 4:17 remaining in the first quarter.
The 49ers finally got on the scoreboard three minutes into the second quarter when fullback Kyle Juszczyk ran for a seven-yard score. Fitzpatrick threw a 22-yard touchdown pass to DeVante Parker on the Dolphins next drive and Miami kicker Jason Sanders made field goals on the next three drives for a 30-7 lead at halftime.
Beathard threw a 19-yard touchdown pass to Kendrick Bourne on the 49ers first drive of the second half. Fitzpatrick hooked up with Preston Williams for a 32-yard touchdown on the Dolphins next drive to give Miami a 37-14 advantage.
49ers kicker Robbie Gould made a 37-yard field goal on the next possession before Sanders added two field goals for the Dolphins' final 26-point lead.
Williams hauled in four catches for 106 yards and a score for the Dolphins and 49ers running back Raheem Mostert had 119 yards from scrimmage on 14 touches.
Bobby McCain and Xavien Howard had interceptions for the Dolphins. Jerome Baker, Andrew Van Ginkel, Elandon Roberts, Emmanuel Ogbah and Zach Seiler each recorded sacks in the victory.
"Our guys showed up and brought a lot of energy," Dolphins coach Brian Flores said. "That's the type of preparation that we need in order to have success in this league.
"I think they're learning that. Hopefully we'll learn that and they'll understand that's what it takes, that's the type of preparation you need. We've got do it every week. This week's great. We'll enjoy it, but we've got to string something together."