Three takeaways from 49ers' 29-27 loss to Chargers

CARSON -- For the first time this season, the 49ers played a full game without franchise quarterback Jimmy Garoppolo, who sustained a season-ending knee injury last week in Kansas City. Backup-turned-starter C.J. Beathard nearly joined him on the sideline.

Beathard took over for what the 49ers hope will be a 13-game run as their starter. It all began Sunday in a 29-27 loss to the Los Angeles Chargers in front of a 49ers-dominated crowd of 25,397 at StubHub Center, although Beathard briefly left after taking a wicked hit in the fourth quarter.

Here are three takeaways from the 49ers’ perspective as they fell to 1-3.

C.J. is OK

The 49ers brought in seven free-agent quarterbacks for workouts last week, but they opted not to sign any of them. The team entered the week with needs at a lot of different positions, and coach Kyle Shanahan is fine with Beathard as the starter and Nick Mullens as the backup.

Beathard showed why Shanahan has so much confidence in him.

This is Beathard’s second full year with the 49ers in Shanahan’s offense, so he likely knows the system better than Garoppolo, who arrived in the middle of last season. Beathard appeared to run the offense well, as he did a good job of moving the chains by going 5 of 12 third-down conversions. He also completed 23 of 37 passes for 298 yards and two touchdowns with two interceptions in his first start of the season.

Beathard threw one of those interceptions in the third quarter as the 49ers drove deep into Chargers territory, but it wasn't his fault, as his on-target pass bounced off tight end Garrett Celek's hand. Chargers cornerback Trevor Williams grabbed the ball and returned it 86 yards to set up a field goal.

Tight end George Kittle, Beathard’s teammate at Iowa, went to great lengths to make up for it with an 82-yard catch-and-run for a touchdown late in the third quarter. Kittle finished with six receptions for a career-high 125 yards.

Beathard had another interception late in the game as Chargers safety Derwin James hit him as he was throwing. Beathard completed 23 of 37 passes for 298 yards with two touchdowns and two interceptions. His passer rating was 82.9.

Injuries piling up

One week after losing Garoppolo to a season-ending torn ACL, the 49ers have more injury issues heading into next week’s home game against the Arizona Cardinals.

The most concerning injury occurred in the second quarter when six-time Pro Bowl left tackle Joe Staley went down with a right knee injury. Staley got rolled up on from behind while in pass protection, and he left the game and was examined. At halftime, the 49ers ruled him out for the remainder of the game. The 49ers believe Staley did not sustain any damage to his ACL.

Backup tackle Garry Gilliam entered the game and played the remainder at left tackle. Right tackle Mike McGlinchey also left the game briefly in the third quarter with a knee injury of his own.

Rookie wide receiver/punt returner Dante Pettis sustained a left knee injury in the first quarter and didn't return to action.

More energy on defense

The 49ers’ defense couldn't have had a better start despite playing with two reserve safeties. The 49ers also did a better job of tackling early in the game after struggling in that area during the first three games of the season. But some of their old problems were apparent later in the game.

Antone Exum, who started for the second time in a row in place of Jaquiski Tartt, intercepted a Philip Rivers pass on the first possession of the game and returned it 32 yards for a touchdown. DeForest Buckner forced the poor throw with inside pressure to get into Rivers’ face as he threw.

Exum punctuated the first TD and first interception of his 32-game NFL career by throwing the ball into the stands, which will subject him to a $6,683 fine from the NFL.

Rookie D.J. Reed made his first career start and got the nod at free safety despite the 49ers clearing Adrian Colbert to suit up. Colbert was listed as questionable before the game because of a hip contusion.

Linebacker Reuben Foster, who missed six tackles last week, put together a solid game and was a factor from the opening sequences of the game.

Left cornerback Ahkello Witherspoon had another rough outing, leading the 49ers to bench him in favor of Greg Mabin in the third quarter. Mabin forced a Melvin Gordon fumble that nearly ended the Chargers' scoring drive after Williams' pick. 

Rivers, who ranks in the top 10 of every significant all-time NFL passing statistic, completed 25 of 39 passes for 250 yards and three touchdowns with one interception.