SANTA CLARA, Calif. — Befitting a season in which almost every step forward has been negated by one in the opposite direction, the San Francisco 49ers had a hard time celebrating the highly anticipated return of standout outside linebacker Aldon Smith to practice Wednesday.

That’s because, once again, their roller-coaster season took a dip of equal magnitude with news that Smith’s sidekick, inside linebacker Patrick Willis, would have to undergo season-ending surgery on his left big toe.

“We were taking it a day at a time. Now the decision’s been made,” 49ers coach Jim Harbaugh said of the surgery and subsequent placement of Willis on injured reserve.

If there’s ever a good time for an All-Pro to be lost for the season, it might be now for the 49ers, who take a 5-4 record to New York to face the Giants on Sunday.

First, they have Smith possibly ready to make his season debut at linebacker this week. They have fellow inside linebacker NaVorro Bowman working out with an eye on returning sometime soon. And they have tackling machine Chris Borland playing exceptionally well in Willis’ spot.

“Chris Borland is acquitting himself extremely well,” Harbaugh said of the rookie, who has been starting alongside Bowman’s replacement, Michael Wilhoite.

“Those two are doing a great job of elevating their game to the standard that NaVorro and Patrick have set around here. I mean, they have no choice really but to do that.”

Borland’s strong play of late had no bearing on the decision to end Willis’ season, Harbaugh assured.

“That’s what Patrick feels is going to be what’s best for his football career and going forward,” Harbaugh said of the surgery. “So that’s the best thing for us.”