SANTA CLARA, Calif. — By many accounts, the San Francisco 49ers have one of the best offensive lines in the NFL.

There was no indication of that watching Sunday’s 28-20 home loss to the Chicago Bears, a daunting debut in their Levi’s Stadium.

Even with right guard Alex Boone returning to his starting spot for the first time since a training-camp holdout, the 49ers had problems up front in just about every aspect of the game.

Quarterback Colin Kaepernick was sacked four times, including twice by Bears backup left end Willie Young, who beat 49ers backup right tackle Jonathan Martin on both occasions. Martin was starting in place of injured Anthony Davis.

The 49ers ran for only 129 yards against a team that allowed the most rushing yards in the league last season (163.4 yards per game). The Bears were trampled for 193 yards in the 2014 season opener by the Buffalo Bills. And the 49ers’ total of 129 is a bit deceiving. Forty-eight of Kaepernick’s team-leading 66-yard total came on mad scrambles during attempts to avoid adding to the aforementioned sack total.

Two penalties on linemen were particularly destructive. A holding call on left tackle Joe Staley negated a 10-yard Kaepernick run, a net 20-yard loss on a first-quarter drive that ended up nine yards short of the goal line. And Martin had a false start on a third-down play at the Chicago 9. The 49ers had to settle for a short field goal two plays later.

The line also failed to come through when given a chance to put the game on their shoulders. Looking to extend a 17-7 lead in the third quarter, the 49ers ran three consecutive times from the Chicago 6-, 5- and 7-yard lines, gaining one yard twice to sandwich a two-yard loss on the second-down play. Instead of getting what might have been a clinching touchdown, the 49ers had to settle for a field goal.

“We as an offense need to pick it up,” Boone assessed after the game. “We can’t leave our defense out to dry like that. We’ve got to get back in the meeting rooms, look at things and get better.”

Martin gave up a sack to Young on the 49ers’ final drive, one that could have tied the game with a touchdown and successful two-point conversion.

“That last drive is obviously not up to par,” he said. “So it’s frustrating. It’s something to improve on. Got to do better next time, next game.”

Martin will go down at the poster boy for Sunday’s issues, a problem that might go away this week as 49ers coach Jim Harbaugh is hopeful of getting Davis back from his hamstring injury. But even the line’s standouts — Staley and left guard Mike Iupati — had their bad moments.

Staley not only had the holding infraction on the 10-yard Kaepernick run but also jumped the snap count once, resulting in an additional five yards in penalties. And Iupati was beaten by Bears defensive tackle Stephen Paea for one of the four sacks.

In all, the Bears had seven tackles for losses and were credited with five “hurries” on Kaepernick pass attempts.

The 49ers suffered two key injuries in Sunday’s loss, both at tight end. Starter Vernon Davis got bent over backward following a fourth-quarter catch and sprained his left ankle. He left the game for good, was carted to the locker room and was seen on crutches later on.

He was sent to Stanford Hospital on Monday for an MRI. Vernon Davis’ status for Sunday’s game at Arizona will be determined later in the week.

Davis had three catches for 39 yards in the game.

His backup, Vance McDonald, injured his right knee in the first half. He was able to return to the game in the second half, but mostly as a blocker and to give third-stringer Derek Carrier a break.

Carrier took advantage of the situation to catch three passes for 41 yards.

REPORT CARD VS. BEARS

–PASSING OFFENSE: C-minus — 49ers quarterback Colin Kaepernick had decent passing numbers (21-for-34, 248 yards) if you throw out the three interceptions and four sacks. He lost one of his favorite targets, tight end Vernon Davis, with a little more than 10 minutes to go. Still, he was able to drive the 49ers into scoring position with a chance to tie the game in the final minutes, only to — fittingly — come up short when his fourth-down pass intended for wideout Michael Crabtree was broken up at the goal line.

–RUSHING OFFENSE: D-minus — One reason Kaepernick had to throw 34 passes in the loss was the failure of the ground game against a team that was supposed to be vulnerable against the run. The Bears had allowed the most rushing yards in the league last season, and were run over to the tune of 193 yards in the 2014 opener against the Buffalo Bills. Throw out Kaepernick’s 48 yards on unscripted scrambles and the 49ers were held to a disappointing 81 yards on 23 carries.

–PASS DEFENSE: C-minus — The Bears took advantage of a mismatch in size when quarterback Jay Cutler found 6-foot-5 Brandon Marshall for three touchdowns against 5-11 Jimmie Ward in Sunday’s win. The 49ers held Cutler to 176 passing yards, but they never intercepted him, and sacked him only once. In the end, his four TD passes trumped everything else.

–RUSH DEFENSE: A-minus — Having watched the Dallas Cowboys have their fair share of rushing success against the 49ers in the opener, no doubt the Bears figured they’d be able to unleash running back Matt Forte on the San Francisco defense Sunday. But Forte wound up being a nonfactor, held to 21 rushing yards on 12 carries.

–SPECIAL TEAMS: A — Had the 49ers beaten the Bears, backup outside linebacker Aaron Lynch would have been one of the stars of the victory. After all, it was his blocked punt following Chicago’s first offensive possession that propelled the 49ers to an early 17-0 lead. Phil Dawson also made both of his field goals in his Levi’s Stadium debut, a good sign going forward.

–COACHING: D — In the end, one of the biggest sequences of plays occurred on the 49ers opening possession of the third quarter, up 17-7. Thanks in large part to 24- and 20-yard completions to wideouts Michael Crabtree and Stevie Johnson, respectively, the 49ers had a first-and-5 at the Chicago 6-yard line, with a chance to go up 17 points. That’s when 49ers coach Jim Harbaugh stubbornly ran the ball three times, twice gaining one yard and once losing two. The result was a field goal that kept the Bears in the game at 20-7 and gave them a bit of momentum leading into their 21-0 finish.