49ers drop exhibition finale with most key players out of action

SANTA CLARA - The Junior Varsity Los Angeles Chargers sent the Junior Varsity 49ers a message during the preseason finale Thursday night.

The message: Our backups are slightly better than yours.

The 49ers lost on the final play - a 36-yard field goal by Chargers backup kicker Robert Aguayo, who gave the Chargers a 23-21 victory.

Most starters for both teams did not suit up, with two big exceptions: Defensive end Solomon Thomas and linebacker Reuben Foster both played. Thomas was on the field for the 49ers’ first defensive series, and Foster for their first three.

Foster played just five days after suffering a concussion during the 49ers’ dress-rehearsal preseason game against the Indianapolis Colts. He immediately entered the NFL’s concussions protocol. The 49ers cleared him Wednesday.

“Once he got out of the protocol and felt good, that’s what we planned on doing as long as he was healthy,” head coach Kyle Shanahan said after the game in the 49ers auditorium.

The 49ers wanted to give Foster extra playing time during the preseason, because the NFL suspended him for the first two regular season games. He violated the league’s policy on personal conduct and substances of abuse during the offseason.

Against the Chargers, Foster finished with two tackles, including one for a 6-yard loss.

Thomas was even more productive against the Chargers backups. First, he tossed third-string tight end Sean Culkin to the side and tackled third-string running back Detrez Newsome for a 4-yard loss. Six plays later, Thomas burst into the Chargers backfield unblocked and tackled fourth-string running back Justin Jackson or a 3-yard loss.

“Thomas wanted to play a little bit more, and I thought it would be good for him,” Shanahan said. “He was able to make a couple of plays and we got him out of there. He stayed healthy. It was a risk, but something that can help him for Week 1.”

Thomas needed extra playing time - he missed the second preseason game with a concussion.

He returned last week for the third preseason against the Indianapolis Colts.

Fellow starting defensive lineman Arik Armstead missed the first two preseason games with a pulled hamstring. Like Thomas, Armstead returned last week against the Colts. But, he did not play against the Chargers.

“I just didn’t think he needed it,” Shanahan said. “He got a lot of playing time last week. Felt good in practice. Didn’t want to risk it.”

The 49ers sat all 11 of their starters on offense, including quarterback Jimmy Garoppolo. Backup quarterback C.J. Beathard started in Garoppolo’s place, played one drive, took one sack and threw zero passes.

Guard Joshua Garnett started at right guard. He is competing for the starting job with Mike Person, who did not play against the Chargers, which suggests the competition is over and Person won it, at least for now.

“He’s still the front runner,” Shanahan said. “We’re happy with Mike. He has done a real good job. That’s why we didn’t dress him tonight. But, we’re real excited about Josh, too. He got a late start, which puts him behind the 8ball with the group. There’s a lot of continuity that goes into O-line play. We major in double-team blocks, and you get used to who’s blocking next to you. So, that’s an advantage someone has from just being here. But, Josh is a talented guy we believe in, and he’s going the right direction. It’s a good problem to have.”

The 49ers’ starting running back Thursday was veteran Alfred Morris, who made his 49ers debut last Saturday against the Colts.

He gained 84 rushing yards in that game against a soft Indianapolis defense.

The Chargers B-team defense was not soft. It limited Morris to just 5 yards on two carries, and shut down the 49ers’ B-team early in the game. The 49ers had negative 18 yards of total offense with 12:04 remaining in the second quarter, and trailed 6-0.

That’s when third-string quarterback Nick Mullens led a 75-yard touchdown drive. He capped it with a 4-yard touchdown run. At that point, the 49ers led 7-6.

But, the Chargers scored the next 14 points. Los Angeles running back Terrell Watson scored a 4yard touchdown run just before halftime. Then, 35 seconds into the third quarter, San Francisco running back Jeremy McNichols fumbled at the 49ers’ 16 and the Chargers recovered. Three plays later, wide receiver Andre Patton caught 5-yard touchdown pass from third-string quarterback Cardale Jones, and the Chargers took a 20-7 lead.

That was the score when 49ers third-string quarterback Jack Heneghan entered the huddle.

The undrafted rookie from Dartmouth led two touchdown drives, including one which lasted 16 plays, and helped give the 49ers a 21-20 lead with three minutes left. The 49ers defense couldn’t hold the lead, but Heneghan played well.

“We haven’t given him a rep in a game yet, and he hasn’t gotten very much in practice,” Shanahan said. “But, he knows everything inside and out, has worked has hard as anyone learning the offense and I think the guys really respect him. He’s a talented guy who deserved the opportunity. I was real happy for him.”

Heneghan won’t make the team – he’s fourth on the quarterback depth chart. The 49ers will cut him along with 47 others by 1:00 p.m. Saturday, the deadline to trim down rosters.