49ers’ defensive linemen Darnell Dockett (90) and Tony Jerod-Eddie (63) pursue Broncos’ quarterback Peyton Manning in the first half in Denver on Saturday. (Jack Dempsey/AP)

49ers’ defensive linemen Darnell Dockett (90) and Tony Jerod-Eddie (63) pursue Broncos’ quarterback Peyton Manning in the first half in Denver on Saturday. (Jack Dempsey/AP)

49ers’ offense remains work in progress

DENVER — Linebacker NaVorro Bowman continued to take giant strides for the 49ers on Saturday, but the offense moved in baby steps once again.

In a 19-12 loss against the Denver Broncos, Bowman, who missed all of last season after a devastating knee injury in the NFC championship game in January, 2014, had seven tackles, including five on the second drive, when he also had both of his sacks.

The Denver defense limited quarterback Colin Kaepernick to no pass completions until the final minute of the first half, which ended with the Broncos ahead 8-3. He was just 2 of 6 for 13 yards and scrambled three times for 53 yards.

Rookie running back Jared Haynes handled the ball only three times from scrimmage, an indication that the one-time rugby star already had earned a spot on the Opening Day roster. He caught one pass for 18 yards and carried twice for no gain. He also had a 12-yard punt return.

Corey Acosta was good from 50, 38 and 29 yards in the second half, the last one giving San Francisco a 12-11 lead with 5:43 remaining.

The 49ers (1-2) played without linebacker Ahmad Brooks, who was placed on leave Thursday after being charged with misdemeanor sexual battery, the latest issue for a roster that’s had major change in the offseason.

DeMarcus Ware sacked Kaepernick in the end zone for a safety in the second quarter, the highlight of another stellar outing by Denver’s defense, which has allowed just six points in 11 drives.

Peyton Manning failed to get the Broncos into the end zone in seven possessions, as Denver rode its stifling defense and good ground game to victory.

All that rest has turned into rust for Manning, who was doomed by protection problems and an interception in the end zone one week after penalties and dropped passes kept him from finding any rhythm.

Manning was 14 for 21 for 124 yards and was sacked three times, twice by linebacker NaVorro Bowman.

Manning isn’t expected to play against Arizona next week, meaning he’ll head into the regular season having directed just two scoring drives — both of them field goals — in 11 possessions this preseason.

At least he’ll have two-time Pro Bowl guard Evan Mathis by then. Mathis signed this week, giving the Broncos’ young offensive line a much-needed addition of experience.

The 39-year-old quarterback  has taken some forced time off this summer, sitting every few days because of his age and to get longtime backup Brock Osweiler some work. General manager John Elway says he’ll take a rusty Manning early on over an exhausted one down the stretch.

Juwan Thompson scored the game’s only touchdown on a 1-yard run with 2:04 left that erased a 12-11 deficit and capped an 80-yard drive engineered by Osweiler. He also ran in the 2-point conversion to make it 19-12.

The Broncos (3-0) reached the 20 three times when Manning was in the game but only managed a pair of Brandon McManus field goals. Cornerback Kenneth Acker intercepted Manning’s underthrown pass to Demaryius Thomas in the end zone.

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