Wide receiver Mario Manningham tore both the ACL and PCL in his left knee, sources told ESPN NFL Insider Adam Schefter.
Manningham, already bothered by a shoulder injury previously, limped out of the locker room Monday on crutches. He was scheduled to have an MRI exam on his left knee after he was tackled low by Leroy Hill and fumbled in the third quarter.
Davis must clear the league's NFL concussion protocol after getting knocked off his feet along the sideline by safety Kam Chancellor on a huge hit that looked legal but drew a penalty for thumping a defenseless receiver.
And defensive lineman Justin Smith's streak of 185 starts ended when he sat out with an elbow injury. Niners coach Jim Harbaugh remained mum on Smith's status, except for saying, "He has not undergone a procedure." Asked if Smith will need surgery at some point, Harbaugh would only say, "We'll see."
San Francisco (10-4-1) already had lost backup running back Kendall Hunter (lower leg), wide receiver and punt returner Kyle Williams (left knee) and defensive lineman Demarcus Dobbs (right knee) to season-ending injuries. Defensive lineman Will Tukuafu added to Harbaugh's headaches when he hurt his back against the Seahawks and did not return, and backup linebacker Clark Haggans missed the game with a shoulder injury.
"I feel our team's leadership, I feel the intellect of the staff, I think the talent of the players, the work ethic of the players will pave the way," Harbaugh said.
Seattle's loud fans flustered quarterback Colin Kaepernick and the coaching staff from the start, forcing the 49ers to call two timeouts and get two delay-of-game penalties in the first half alone. Kaepernick completed 19 of 36 passes for 244 yards and a touchdown with one interception in the end zone.
What do the 49ers have to do offensively to avoid penalties and clock-management problems?
"Fix it," Harbaugh said.
"That's the only option we have," left tackle Joe Staley said. "You learn from the film, you watch it and make the corrections. Our whole team didn't play well."
"Rather than go position by position, or any one particular phase, I don't think anybody looks back on this and feels like it was good enough," said Harbaugh, handed a miserable loss on his 49th birthday by longtime rival and Seattle coach Pete Carroll.
San Francisco will look to bounce back to secure both a division title and a first-round bye with a victory over the Arizona Cardinals.
The only way the 49ers can secure a No. 2 playoff seed is a win against the Cardinals coupled with a Green Bay loss at Minnesota. If they lose and Seattle (10-5) wins at home against St. Louis, the Seahawks will steal the division and send San Francisco on the road for the first round.
Information from The Associated Press was used in this report.