That session went well enough for Garoppolo that he followed it up by participating in Wednesday's practice on a limited basis.
But Garoppolo wasn't exactly feeling his best after the session. Asked Wednesday what it feels like to throw with his thumb injury, Garoppolo didn't mince words.
"F--- it, it hurts," Garoppolo said with a laugh. "I don't know how else to describe it. It feels like the web in your hand is kind of tearing a little bit."
Even with Garoppolo back at practice, coach Kyle Shanahan said rookie quarterback Trey Lance was still expected to take the majority of the reps in what was a lighter practice.
The Niners are facing another week of quarterback uncertainty as they prepare for a potential make-or-break game Sunday against the Los Angeles Rams.
"I haven't made [a decision on the quarterback] now, which is the truth," Shanahan said. "And I probably will make it before the game starts, and I will not tell you guys when I do."
The 49ers went through a similar process last week before playing the Houston Texans, though it was clear all along that Lance was going to start because Garoppolo did not participate or throw leading up to that game.
Things figure to be a bit murkier now that Garoppolo has resumed throwing and presumably will continue to practice in some capacity this week.
Garoppolo called Tuesday a "pretty good throwing session," noting that he was trying to get his passing motion back while working with a modified tape job on his right hand.
After Garoppolo suffered the injury in the second quarter of San Francisco's loss to the Tennessee Titans, he said he had to alter his throwing motion to ensure a better grip on the ball and manage the pain in his thumb. But he's hoping to get back to a more normal motion, given the time he has had to recover.
Still, Garoppolo understands he won't be at full strength this week no matter what happens in the coming days.
"Any injury you're definitely not 100%," Garoppolo said. "It's one of those things where it's literally a day-by-day thing. Yesterday it felt good, woke up this morning after throwing and it didn't feel so hot. So each day will be different. It's just about rehabbing it, getting the swelling down, getting the motion down, all those little things."
Although Lance performed well in the win against the Texans -- he was 16-of-23 for 249 yards with two touchdowns and an interception for a passer rating of 116.0 -- Garoppolo has had success against the Rams during his time with the Niners.
Since arriving in 2017, Garoppolo has not lost in five starts against the Rams, and he posted a season-best 96.1 QBR against them in a 31-10 victory Nov. 15. The Niners and Garoppolo still won't push too hard this week if he's not feeling up to it.
"We've got to be careful," Shanahan said. "I think waiting until we did definitely helped get him to this point, but I think each day is a new experience with it, so it's going to be mainly at Jimmy's pace and just talking to him and making sure he doesn't push it too hard to give him a chance for Sunday."
A victory Sunday would clinch a playoff berth and the No. 6 seed in the NFC for the Niners. A loss would leave them hoping for the New Orleans Saints to lose to the Atlanta Falcons so they could sneak into the postseason. Those are the kind of stakes the 49ers haven't had since 2019 -- and the kind that make Garoppolo want even more than usual to be available.
"It's just a long season, a lot of things happened. ... You go through all that stuff just to get an opportunity that we have this Sunday," he said. "That's all you can ask for. I'm going to do everything I can to be out there. It's a big one. Whatever I can do to be out there, I'm going to be out there.
"But at the same time, you've got to be smart and think about what's going to be best for the team to win. So you have just got to be smart with all the decisions you make."