SANTA CLARA — Jim Harbaugh kept his sentences short and information at a minimum Monday, repeating a phrase he will rely on following the worst loss of his NFL coaching career: regroup, refit and reorganize.

That’s all the San Francisco 49ers can do at this point.

Beat up and beat down, San Francisco’s 42-13 blowout loss at Seattle cost the 49ers (10-4-1) more than just a game. They have another pair of key starters questionable with injuries, let control of a first-round playoff bye slip away and head into Sunday’s regular-season finale at home against Arizona (5-10) with a slim half-game lead in the NFC West.

“No excuses or justifications,” an overwhelmingly grim, tight-lipped and humbled Harbaugh said back at 49ers headquarters. “Our team needs to bounce back.”

The only way the 49ers can secure a No. 2 playoff seed — and the first-round bye that comes with it — 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.

Complicating matters even more, the 49ers enter the finale with its depth depleted.

Wide receiver Mario Manningham, who had been bothered by a shoulder injury previously, 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. Tight end Vernon 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 straight starts ended when he sat out with an elbow injury. Harbaugh remained mum on Smith’s status, other to say that “he has not undergone a procedure.” Asked if Smith will need surgery at some point, Harbaugh would only say “we’ll see.”

San Francisco 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.

There are still plenty of problems for the 49ers who are healthy.

Seattle’s rabid 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.

Frank Gore was held to just 28 yards on six carries after rushing for a season-high 131 in San Francisco’s 13-6 win against Seattle in Week 7. The loss of Justin Smith seemed to affect the entire defense, most notably Aldon Smith, who is still stuck on 19 ½ sacks after getting locked up by Seattle’s Russell Okung.

Red Bryant also blocked David Akers’ 21-yard field-goal attempt, Richard Sherman scooped up the ball and sprinted untouched for a 21-0 lead that put the game out of reach.

“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 Sunday by longtime rival and Seattle coach Pete Carroll.

If there’s a bright side to San Francisco’s setback, Harbaugh is 7-0 after a loss in his two-year tenure and competition will not be nearly as difficult as the last two weeks at Seattle and New England.

The 49ers routed the Cardinals 24-3 in the desert on Monday Night Football on Oct. 29, a game Alex Smith completed 18 of 19 passes for 232 yards and three touchdowns. Smith has since been replaced by Kaepernick, a high-risk, high-reward, dual-threat quarterback who is 4-2 as the starter.

While the 49ers also have looked dominant at times this season, they still have yet to put together a winning streak. Five times this season San Francisco has won two consecutive games, and five times they have failed to win the third game, including a 24-24 tie against St. Louis in Week 10.

To win the Super Bowl — or even just get there — the 49ers will have to change that.

“We’re going to move forward,” Harbaugh said. “No explanations. No excuses necessary.”