Come Monday morning, that was no longer the case. Hufanga has entered the concussion protocol, according to coach Kyle Shanahan.
That comes after Hufanga was evaluated for a head injury on Atlanta's first offensive series and passed the tests to return to the game.
"He passed it then," Shanahan said. "He passed one after the game, but then there's always a third one the day after the game. And he came in with some symptoms today, so that's why he's in [the protocol]."
League protocols allow for what is called "delayed onset," which means Hufanga must go through the standard protocol in order to be cleared to play again. His availability for next week's game against the Kansas City Chiefs depends on how he feels as the week goes on.
Hufanga has been an early-season revelation for San Francisco's defense, posting 36 tackles, a sack, two interceptions (one returned for a touchdown) and five pass breakups in his first six games as the full-time starting strong safety.
For the Niners, Hufanga's injury is just the latest in an increasingly long list of ailments, particularly on defense. As it stands, linebackers Fred Warner and Dre Greenlaw are the only healthy starters among the 11 players the Niners envisioned for their defense entering the season.
Linebacker Azeez Al-Shaair (knee), defensive tackle Javon Kinlaw (knee) and cornerback Emmanuel Moseley (knee) are on injured reserve, while end Nick Bosa (groin), defensive tackle Arik Armstead (foot, ankle) and free safety Jimmie Ward (broken left hand) did not play in the 28-14 loss to Atlanta because of their injuries.
Cornerback Charvarius Ward suffered a groin injury in the loss to Atlanta and did not return, though Shanahan said he'll be day-to-day this week and could be available against the Chiefs. The same is true of right tackle Mike McGlinchey, who has a bruised left calf, and defensive ends Drake Jackson (knee sprain) and Samson Ebukam (Achilles tendinitis).
If there's a silver lining to be found, it's in the hope that some reinforcements are on the way. Shanahan said Monday he is hopeful Bosa and offensive tackle Trent Williams (right ankle sprain) could be ready to play against the Chiefs.
"I'm really hoping for it," Shanahan said. "I think there's a decent chance."