SANTA CLARA (AP) — The San Francisco defense dearly misses the menacing presence of suspended pass-rushing specialist Aldon Smith, and it better get used to it.

Smith is just two games into his nine-game penalty from the NFL for violations of league substance-abuse and personal-conduct policies.

This unit realizes it must find ways to put more pressure on the quarterback without Smith and avoid the costly big plays and penalties like those surrendered in a stunning 28-20 loss Sunday night to the Bears in the Levi’s Stadium opener.

“We definitely miss Aldon. Any team would miss Aldon Smith,” defensive tackle Tony Jerod-Eddie said Tuesday. “He’s one of a kind, one of those guys every 10-12 years. We’re definitely capable with (Dan) Skuta and Corey Lemonier and even Aaron Lynch.”

The 49ers managed just one sack of Chicago’s Jay Cutler, who threw three fourth-quarter touchdown passes to rally his team back from a 17-0 deficit. That’s after San Francisco sacked Tony Romo three times in a Week 1 win at Dallas.

There’s another big test ahead Sunday at unbeaten Arizona (2-0), the early leader in the NFC West after defending Super Bowl champion Seattle lost at San Diego and the 49ers fell to the Bears later in the day.

After a day off Monday, the Niners reunited at team headquarters for film study in an effort to figure out what went wrong and how they can fix it fast.

Some of the problems came from penalties on third down that kept the defense on the field. San Francisco had 16 penalties for 118 yards.

“Those penalties, man, they hurt us big time,” linebacker Patrick Willis said. “We had a lot of opportunities where we had a chance to get off the field and you turn around and see the flag. It’s kind of like a punch in the gut. Regardless if it’s against you, if it’s against us, then we got to line up and try to get off the field again. But anytime you got a chance to get off on third down and you get a penalty, it’s rough. It hurts.”

Cornerback Tramaine Brock walked through the locker room with a boot on his right foot protecting his injured toe, raising doubt he will be ready to return by Sunday. Tight end Vernon Davis is nursing a left ankle injury that had him on crutches after the game.