Jimmy Garoppolo injured his left knee while on a third-down scramble.
Garoppolo wound up playing his best game of the season Sunday, throwing two touchdowns against zero interceptions, completing 66.6 percent of his passes and finishing with an impressive 114.7 passer rating, albeit against a suspect Chiefs defense.
"With Jimmy we're fearing ACL", Shanahan said. "I haven't got a chance to see him yet, but I feel for him".
Garoppolo's left knee buckled just before the Chiefs' cornerback delivered a shoulder-to-shoulder blow, sending Garoppolo down.
Garoppolo took a big hit up high, but the damage appeared to be a non-contact injury before he took the hit.
The 49ers made Garoppolo the highest-paid player in the National Football League, at the time, when they signed him to a five-year, $137.5 million deal during the offseason.
The 49ers (1-2) visit the Los Angeles Chargers (1-2) this Sunday at 3:25 p.m.
After gaining 13 yards, Garoppolo had the choice between stepping out of bounds or staying in and taking a hit from a defender.
Beathard said he spoke to Garoppolo briefly in the trainer's room, and what little of their exchange he was willing to repeat made it quite clear the 49ers' franchise quarterback - who signed a five-year, $137.5 million extension in February - expects his season to be over.
Top cornerback Richard Sherman went down with a calf injury, while backup Tarvarius Moore left with a wrist injury. "He's a man out there, and he's a very good quarterback; and we're fortunate to have him".
49ers: The defensive backfield was in tatters by the fourth quarter.