SANTA CLARA, Calif. (AP) -- Colin Kaepernick donned a red cap and sneakers, offered a quick side hug to third-string quarterback Dylan Thompson, then took his spot on the sideline for the San Francisco 49ers' 14-12 win against San Diego on Thursday night.

The 49ers will go into the regular season with significant questions about their offense after Kaepernick and the first team unit failed to score a touchdown on eight preseason possessions, and they didn't play in this one. Their next test will be in the season opener Sept. 14 against Minnesota.

"We need the practice time instead of going out there today," coach Jim Tomsula said. "Coming into this for five or six plays, I thought it would be better if we were able to get to 45 or 47 plays yesterday and then be able to get those again tomorrow."

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Bruce Ellington showed he appears back to full strength following a right hamstring injury, while former Australian rugby league star Jarryd Hayne made his case for a spot on the 53-man roster.

Ellington caught a 70-yard touchdown pass on the third snap of the game when he ran about 65 yards following a quick slant. The Niners then converted a 2-point conversion to Quinton Patton.

Hayne carried 10 times for 58 yards, caught a pair of passes for 17 yards, and returned three punts for 43 yards.

Tyrell Williams caught a 63-yard touchdown pass from Brad Sorensen in the fourth quarter, but the Chargers missed the 2-point conversion to tie the game.

"We've got some great receivers, so I just hope good things come from it," Williams said.

San Diego's Richard Crawford had a 29-yard interception return for a touchdown in the second quarter. He picked off a pass by Thompson by jumping in front of DeAndrew White, while Cordarro Law came untouched at Thompson through the second-team Niners offensive line.

White took a punishing hit from Adrian Phillips returning a punt 34 yards late in the second quarter.

Chargers backup quarterback Kellen Clemens was 10 of 17 for 64 yards.

Ellington had a punt return of approximately 60 yards called back for a penalty. While Ellington would like to be the punt returner again, he said of Hayne, "He can help us a lot."

Some observations from the game:

MR. AUSSIE: Hayne made a pretty cutback on a 19-yard run late in the third quarter. On a 12-yard catch a few plays later, Hayne didn't budge when Lowell Rose tried to make a tackle on the sideline. Hayne just lowered his shoulder as the defender went down. That had his mother and sisters in smiles as they watched from the stands at Levi's Stadium.

"Jarryd's a tough guy," Tomsula said.

Hayne also had a tackle on Javontee Herndon when he beat a double-team on return coverage. Late in the game, Hayne had his first fair catch so far, as instructed.

Tomsula said Sunday on the heels of a loss at Denver that he had seen everything he needed to evaluate Hayne, who emerged through a strong training camp as a contender to make the 53-man roster, which will be announced Saturday.

"I saw him catch passes, I saw him run the ball. The running there were some really good plays," Tomsula said. "I saw him tackle in coverage units, I saw him catch balls and return balls."

THE 53-MAN ROSTER: Chargers coach Mike McCoy knows how tough it will be to pick his final roster, and expected things still to change before Saturday's cutdown.

"A lot of guys are very deserving. They've done a great job," he said. "I just can't be happier with the football team, with the effort and the energy and the way they played from the first day of the offseason to tonight."

FIELD FOCUS: Approximately half of the field appeared replaced following last Saturday's Luke Bryan concert, though the team hasn't said which grass company it used this time. The entire Levi's Stadium grass is scheduled to be re-sodded ahead of the home season opener.

SITTING OUT: Quarterback Philip Rivers and most of San Diego's starters didn't play. Not dressing for the 49ers were defensive lineman Darnell Dockett, wide receiver Torrey Smith, cornerback Tramaine Brock and tight end Vance McDonald.

Newcomer Smith has been dealing with a knee injury.