SAN FRANCISCO – You know a team has high expectations for the season when more than half of its starters emerge from the locker room at the start of the exhibition finale without their helmets.

The 49ers who sat out Thursday's 35-3 win against San Diego included the entire starting defense, running back Frank Gore and wide receivers Randy Moss, Michael Crabtree and Kyle Williams.

Quarterback Alex Smith and the starting offensive line began the game. But Smith left after five plays, all of them handoffs that ensured that Smith, who absorbed some wicked hits in the first three preseason games, would remain untouched in this one.

From there, backups Colin Kaepernick and Josh Johnson beat up on the Chargers, including, in Kaepernick's case, San Diego's first stringers.

"You always want to go out there and move the ball," Kaepernick said. "Knowing it was against their starters makes it feel even better."

For the last decade or so, the 49ers were a rebuilding team that needed to give their starters a lot of snaps in the fourth preseason game. Their usual fourth-game opponent, San Diego, typically would sit quarterback Philip Rivers and the other starters.

This time it was Rivers and the Chargers' starters going against the 49ers' backups during the first quarter. And the 49ers' reserves had the upper hand.

On the Chargers' first drive, safety C.J. Spillman stripped tight end Antonio Gates of the ball, which was picked up by fellow safety Trenton Robinson and returned 22 yards. On the Chargers' ensuing drive, Rivers was intercepted by another backup safety, Darcel McBath.

With Smith on the sideline, the focus Thursday was on the 49ers' backups.

After Robinson's fumble recovery, Kaepernick nearly hit Brett Swain deep on the right sideline. One play later, he ran forward out of the pocket, kept his head up and saw that Delanie Walker had gotten behind the linebacker covering him.

Kaepernick threw a dart along the left sideline to Walker, who broke through Chargers safety Atari Bigby's tackle and then did a falling tap dance into the end zone.

It was the first touchdown pass for Kaepernick in a 49ers uniform. Kaepernick got touchdown No. 2 in the second quarter when on third down he bought extra time by rolling out to his right before finding rookie A.J. Jenkins by himself in the back of the end zone. The 12-yard touchdown was Jenkins' first as a 49er.

Throughout the first half, Kaepernick showed why the 49ers used a high, second-round draft pick on him: He's excellent at evading defenses with his quick feet and then making them pay with his big arm. He finished 12 of 18 for 158 yards and had a 131.3 passer rating. Jenkins led all receivers with four catches for 59 yards.

In the second half, coach Jim Harbaugh and the 49ers let Scott Tolzien and Johnson continue their battle to be the 49ers' third quarterback this season.

Like Kaepernick, Johnson was excellent on the run, and after missing three potential big plays in the last two games, he finally got one in the finale.

And it only took one play.

From the San Francisco 49-yard line, he fired a quick screen to rookie wideout Nathan Palmer, then watched as Palmer sprinted into the end zone for a 51-yard touchdown. On the next possession, Johnson led a 12-play drive before finding rookie tight end Garrett Celek in the back of the end zone.

Johnson finished the game 9 of 14 for 125 yards and a 132.4 passer rating.

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