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SAN DIEGO – Perhaps the biggest victory in any preseason finale can be found on the injury report, not on the scoreboard. But for those interested in the final score of the 49ers’ road matchup with the San Diego Chargers on Thursday night, the visitors were victorious 20-17.

As for the all-important health score, the 49ers fared pretty well in that regard, too. Only second-year linebacker Keaton Kristick’s injury in the second quarter was a downside in the 49ers’ second preseason victory of 2011.

And while many look to get through the final preseason contest with their health intact, the 49ers looked to improve on last week’s 30-7 loss to the Houston Texans. They did just that, scoring on their opening two possessions against San Diego’s respected defense. 49ers coach Jim Harbaugh attributed much of the success to the offensive line.

“I was definitely pleased with the way the ones played,” Harbaugh said. “I thought they played with a lot of urgency and they challenged themselves all week. It was a short week, but it was a good week.”

Following the game, Harbaugh said it was safe to say Alex Smith would be the starting quarterback for the Sept. 11 opener, when the 49ers will host the Seattle Seahawks.

As a whole, the 49ers looked sharp on the evening, even with limited use of their significant players. Running back Frank Gore and tight end Vernon Davis began the game with the first-team offense, but neither touched the ball on the opening drive. Gore didn’t play at all last week against Houston; Davis missed two days of practice this week due to personal matters.

But it didn’t quite hurt the 49ers offense, especially on a night where Smith came out firing on all cylinders.

The San Diego native led the 49ers down the field on the game’s opening possession with an 80-yard touchdown drive. Second-year running back Anthony Dixon capped the possession with a 1-yard run behind the blocks of right guard Chilo Rachal and right tackle Anthony Davis.

“We definitely wanted to get the taste out of our mouths from last week,” Smith said. “Knowing that you’re getting limited plays, it’s definitely the way you want your only drive to go.”

The first-team offense ran 14 plays for their first touchdown of the preseason and it was due in large part to the mauling play of its offensive line. The maligned unit gave Smith time to throw and also paved the way for rookie running back Kendall Hunter, who carried 6 times for 46 yards on the impressive opening drive.

The 49ers offense went right back on the field after linebacker NaVorro Bowman sacked Chargers quarterback Billy Volek and recovered the subsequent fumble. Starter Philip Rivers sat out of the game, along with other key offensive starters.

“It was just a basic blitz,” Bowman explained. “I had the running back on me one-on-one and that’s something a linebacker wants to get when trying to get a sack.”

Following Bowman’s turnover, the 49ers had the ball at San Diego’s 22-yard line. From there, the 49ers marched their way to the end zone once more, putting an exclamation mark on their final preseason performance.

Dixon scored his second, 1-yard touchdown run of the night to punctuate the physical drive. This time, he stayed low behind fullback Moran Norris’ lead block to plunge his way into the end zone.

“The O-line played great,” Smith said on a night where the 49ers rushed for 164 yards. “The guys up front, I think they got challenged this week a little bit, and they stepped up to it.”

Smith played just two series, finishing the night completing 8 of 10 passes for 45 yards with a quarterback rating of 85.4.

Despite the success Smith enjoyed, rookie backup Colin Kaepernick had a rockier start to his performance.

After San Diego responded with a touchdown of their own, on a 56-yard scamper from running back Ryan Mathews on the opening play of the second quarter, Kaepernick threw two interceptions in the second quarter.

On Kaepernick’s first drive in the second quarter, he was intercepted when his corner route intended for wide receiver Lance Long was picked off by Chargers rookie cornerback Marcus Gilchrist in the end zone.

Kaepernick later avoided two sacks on the 49ers ensuing possession, but could not keep the ball away from his opponents. The rookie signal-caller forced a slant pass to a well-covered Ronald Johnson. As a result, the ball was tipped initially and intercepted by Chargers cornerback Dante Hughes inside of 49ers territory.

The trend of second quarter turnovers continued when San Diego rookie running back Jordan Todman fumbled a handoff as defensive end Demarcus Dobbs punched the ball loose for linebacker Alex Joseph to recover. Outside linebacker Aldon Smith, San Francisco's first-round pick out of Missouri, capped off his preseason with a 2.5-sack performance on Thursday, garnering praise from Harbaugh.

"I saw him play with some passion tonight, some emotion," Harbaugh said. "The light's coming on more and more and he's making really good progress."

Though Kaepernick struggled initially, he rallied the offense in the second half. Kaepernick led the 49ers on a 10-play, 49-yard drive which resulted in a 49-yard field goal from veteran kicker David Akers. The successful try gave the 49ers a 17-7 lead with 6:36 left in the third quarter.

The Chargers added a third-quarter field goal from kicker Nate Kaeding from 23 yards out.

Veteran Josh McCown entered the game late in the third quarter for the 49ers to make his first preseason appearance of 2011. His drive set up a 26-yard field goal from Akers. Quarterback McLeod Bethel-Thompson also made his preseason debut.

The Chargers made things interesting late, scoring a touchdown with 1:21 left in the game to cut their deficit to 20-17. San Diego tried an onside kick on the ensuing kick-off, but backup receiver Joe Hastings fell on the ball to clinch the victory.

The 49ers will announce final roster cuts on Saturday when they trim the roster down from 80 players to 53.