If there were any lingering questions as to why San Francisco 49ers coach Jim Harbaugh and GM Trent Baalke "evaluated" Peyton Manning in the offseason, they were answered Sunday as Manning shredded the 49ers' first-team defense in a little less than a quarter of play.

Manning looked like the Manning of old by completing 10 of 12 passes for 122 yards and a pair of TDs as the Broncos built a 17-0 with their first-team offense.

The 49ers were without starting LBs NaVorro Bowman and Aldon Smith, but the performance has to be unsettling for DC Vic Fangio, who brings back the entire starting unit from last year. Denver's first-series FG marked the third straight time this preseason the 49ers' starting defense allowed a FG on the first possession of the game. The unit has allowed points on six of seven preseason series.

"I don’t want to say it’s just the preseason because this is the time to get better," LB Ahmad Brooks told Eric Branch of the San Francisco Chronicle. "This is the time you can really showcase what your team is capable of doing. It’s been a scary start to [this] point."

There was a noticeable lack of pressure on Manning, who seemed to have open receivers to throw to on each of the three series he played.

Bowman and Smith made the trip to Denver and took part in pregame warmups but did not stay in pads for the game. Both players are expected to be able to play by the time the regular season opens at Green Bay on Sept. 9.

The first-team offense didn't fair much better. QB Alex Smith's numbers (5 of 7, 69 yards, 1 TD) appear OK, but the offensive line played poorly in both pass and run blocking. While Manning was nearly flawless, Smith had his ups (a 44-yard TD pass to Vernon Davis) and his downs (a fumbled center exchange with Jonathan Goodwin).

It wasn't until the starters were out of the game did the 49ers come back to win 29-24.

Kaepernick showing improvement: QB Colin Kaepernick turned in the best game of his young career by completing four of four pass attempts for 80 yards. He showed why many consider him to be an intriguing prospect on a play where he eluded pressure -- Harbaugh said it was botched protection -- rolled to his left and threw on the run to TE Konrad Reuland for a first down.

No. 3 QB job still up for grabs: Despite being listed at No. 4 on the team's official depth chart, second-year pro Scott Tolzien was the third QB to play -- ahead of Josh Johnson. He completed one of four pass attempts for 16 yards, while Johnson missed on his only pass attempt. 

Tolzien seems to have the edge as training camp winds down, but the coaching staff has been mum on which player has a leg up. Johnson was the third QB to play last week against Houston, but Tolzien was third in the preseason opener against Minnesota.

"Both have done some really good things," Harbaugh said. "Not ready to make that call yet."

Akers in 2011 form: The 49ers rode K David Akers' NFL-record 44 FGs to a 13-3 regular-season record last year and picked up where they left off Sunday. Akers was good on FGs of 33, 45, 21, 32 and 44 yards.

Manningham mourns loss of grandfather: WR Mario Mannginham did not travel to Denver because he was mourning the loss of his grandfather, who passed away this week. The free-agent acquisition from the Giants" data-canon="New York Jets" data-type="SPORTS_OBJECT_TEAM" id="shortcode0"> did not play in the team's first preseason game either.

Ginn's injury not serious: WR Ted Ginn Jr. left the game in the third quarter with an apparent ankle injury, but X-rays came back negative.

Dixon auditioning well: It's still hard to envision a scenario in which RB Anthony Dixon remains with the 49ers, but he's made the most of his playing time the last two weeks. He carried the ball 11 times for 54 yards, including a 26-yard TD in the third quarter, against Denver.

With the depth the team has at RB, Dixon will likely be the victim of a numbers game. With that understood, the 49ers are doing well by the third-year pro by showcasing him for potential suitors in the league.

Follow 49ers reporter Kyle Bonagura on Twitter: @cbssportsnflsf and @KyleBonagura.

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