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SANTA CLARA – The 49ers finally found the end zone in this 2014 preseason, and they finished Sunday afternoon by beating the visiting San Diego Chargers 21-7 at Levi’s Stadium.

So why didn’t it feel like a decisive victory?

Perhaps because the 49ers’ first-teamers (for the most part) were outgained by the Chargers’ first-teamers (for the most part), 121 yards to 69 yards, and were outscored 7-3. And because the starting offense, led by quarterback Colin Kaepernick, still has not scored a touchdown this year. And because two weeks before the start of the regular season, the offensive line looks ragged. And because San Diego quarterback Philip Rivers completed 90 percent of his passes.

OK, let’s give the Niners their due. They won this game, and they did some good things to seal that achievement.

“It feels great to get a win,” tight end Vernon Davis said. “We’ve been struggling a little bit. But like I said, I like to stay optimistic about everything. And I think we have a pretty good chance.”

Backup 49ers running back Carlos Hyde looked sharp, especially on a 20-yard burst in the second quarter. Backup quarterback Blaine Gabbert, a target of derision after the first two weeks of the preseason, was much more effective against the Chargers; he completed 7 of 11 passes for 66 yards and capped a long drive with a touchdown pass to tight end Vance McDonald. The first-team defense stopped the Chargers on a fourth-and-1 play from the San Francisco 5-yard line, and the defensive reserves were consistently stout. Plus, kicker Phil Dawson nailed both of his field-goal attempts after going 0 for 2 against the Broncos a week earlier.

McDonald’s touchdown gave the 49ers a 10-7 lead just before halftime, and they padded it to 13-7 on Dawson’s 28-yard kick at the start of the fourth quarter. Rookie Glenn Winston scored on a 27-yard run with 10:34 to play, and the Niners added a 2-point conversion on Josh Johnson’s pass to Lance Lewis.

The defense snuffed out the Chargers’ final thrust inside of the 2-minute warning when cornerback Darryl Morris intercepted a pass by San Diego backup quarterback Brad Sorensen.

But this being the third preseason game – the one in which the starters tend to see more extensive action – most of the attention was on the first units. And those units were decidedly meh.

Rivers carved up the 49ers secondary a bit – particularly strong safety Craig Dahl, who was filling in for the injured Antoine Bethea (concussion) – and the tackling was inconsistent. Linebacker Aldon Smith let a couple Chargers squirm away.

Most troubling by far, though, was the performance of the Niners’ offensive line. Considered one of the team’s strengths over the past couple years, the front wall seems to be in desperate need of patching.

That isn’t entirely surprising when you consider that untested Daniel Kilgore has taken over at center, castoff Jonathan Martin is playing in place of injured Anthony Davis at right tackle and young Joe Looney is manning right guard instead of Alex Boone, who is holding out in a contract dispute.

But the 49ers’ troubles didn’t necessarily come at those spots. It was the left side of the line that did most of the leaking Sunday. Left guard Mike Iupati, a Pro Bowl pick the past two seasons, was thoroughly abused by the Chargers.

Defensive end Corey Liuget twice beat Iupati to hit Kaepernick, and one of those hits resulted in a fumble that San Diego’s Kendall Reyes recovered at the 49ers’ 14-yard line.

Davis said that when the San Francisco offense finds its “zone,” it will take off.

Asked whether they were in the zone yet, Davis replied: “You know what? It’s still training camp. Still training camp. Very excited about where we are as a team, as an offensive unit. And I think we still have plenty of room to grow.”

Things got so dicey Sunday that the Niners pulled Iupati for a possession midway through the second quarter, replacing him with veteran Adam Snyder. Iupati was back at left guard the next time the 49ers had the ball, and head coach Jim Harbaugh downplayed the substitution after the game.

Kaepernick absorbed a lot of punishment in his quarter-and-a-half of play. He also got nailed by Reyes on an early scramble. Kaepernick coughed up the ball on that play, too, but officials ruled that his knee touched the ground first.

“He’s playing football. Yeah, I would like to see that avoided, but you can’t necessarily program that,” Harbaugh said. “You’ve gotta play the game.”

It was a mixed bag for the 49ers, and we aren’t likely to get much clarity Thursday when they play their final preseason game at Houston. The starters aren’t expected to play much. They will go into the regular with the confidence of a team that has been to the NFC championship game three straight years, but also with several nagging questions.

More praiseworthy, perhaps, was the Levi’s Stadium grass. Most of it was installed Thursday, after the original sod proved unreliably loose.

“I think it’s amazing what the guys were able to do in such a short window,” Dawson said. “So they deserve a lot of credit for being able to put a field together post-Wednesday. Hats off to them.”

And hats off to anyone who can figure out this team right now.

You can reach Staff Writer Phil Barber at 521-5263 or phil.barber@pressdemocrat.com.