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SANTA CLARA — I’m not sure what Thursday night’s game at Levi’s Stadium should be titled, but I know the subtitle: How Kyle Shanahan Stopped Worrying and Learned to Trust His Quarterback.

The 49ers lost again, 41-39 to the Rams this time, in an unexpectedly entertaining slugfest. They’re 0-3 now, and they did many things poorly in this game. But there were some highly encouraging developments in Loss No. 3, and foremost among them was the Niners’ head coach developing some faith in Brian Hoyer.

It took a while.

About five minutes into the second quarter, San Francisco trailed the Rams 17-7 but was gifted great field position when LA’s Tavon Austin coughed up a punt and long snapper Kyle Nelson recovered for the 49ers at the Rams’ 12. The Niners fired several rounds into their feet, though, with left tackle Joe Staley committing a false start and fullback Kyle Juszczyk holding on a run play and rookie tight end George Kittle dropping a pass around the 5-yard line.

So the 49ers soon were staring at third-and-18 at the Los Angeles 20-yard line. Shanahan’s reaction? Wave the white flag. He called a handoff to Carlos Hyde, who gained 2 yards. Robbie Gould came on for a field goal.

After the game, Hoyer downplayed the handcuffs that had been clasped around his wrists.

“It’s third-and-18, I mean, in the red area,” Hoyer said. “Your chances of converting that are probably pretty low. They know you’re just trying to kick a field goal. I really don’t know a play anyone could call there. Maybe you bust a screen.”

But when Aaron Rodgers or Derek Carr or Drew Brees or, hell, even the Rams’ Jared Goff faces third-and-18, he gets a crack at making something happen. He might be on a shorter leash than usual, might be reminded to throw the ball away if no one breaks open immediately. But he gets a shot.

Brian Hoyer did not.

Later, about midway through the third quarter, the 49ers found themselves with a second-and-goal at the Rams’ 1 after a 5-yard run by Hyde. Shanahan fed his halfback again, up the middle, and he was stuffed for no gain. On third-and-1, the Rams must have figured the ball was going back to Hyde. And indeed it was. This time LA linebacker Alec Ogletree was the first to hit him in the backfield, and the Rams swarmed him again at the 1.

Los Angeles led 27-13 at this point, so Shanahan decided to go for it on fourth down. You’ll never guess what came next. OK, you guessed. Carlos Hyde up the middle. This time he scored, and the 49ers were within a touchdown again.

Shanahan’s play call worked, so it’s hard to fault him. But once again he had demonstrated a gaping lack of confidence in his quarterback.

And let’s be honest. Shanahan had every right to be suspicious.

Hoyer had spent much of his first 10 quarters with the 49ers making you wince. In each of the first two games, he threw an interception in the short zone when he failed to anticipate a linebacker breaking to the receiver.

It wasn’t a linebacker this time, but Hoyer again put his team in a hole on Thursday. And this time he decided to get it out of the way immediately. On the first snap of the game, he locked eyes on wide receiver Marquise Goodwin as if he were the only player on the field, and Rams cornerback Nickell Robey-Coleman was all over it. He intercepted the pass with a head start and ran it back to the 49ers’ 3.

The second play of the game was a touchdown run by Los Angeles’ Todd Gurley.

“The guy made a good play. He guessed right,” Hoyer said of the interception. “We’re thinking with Marquise going over there, the speed that he has, the guy’s gonna back way off. And he just decided to sit on it. So you chalk it up to the guy making a good play.”

Hoyer settled down after that, but was far from perfect. Early in the second quarter, for example, Pierre Garcon broke open down the left side of the field, and Hoyer’s throw was too far and out of bounds.

All along, Shanahan has been one of Hoyer’s most ardent supporters. The quarterback had previously played for him in Cleveland, where Shanahan was the offensive coordinator in 2014, and the coach handpicked him to be his caretaker in Santa Clara until he can find a true franchise QB. Many times since March, when the 49ers signed Hoyer, Shanahan had expressed certainty in the passer.

But his play calls were saying otherwise.

Then came the fourth quarter — a heck of a fourth quarter, too, with four touchdowns, a failed 2-point conversion try and a successful onside kick — and Shanahan seemed to experience a change of heart.

The period started with the 49ers deep in Rams territory, and when they got to the visitors’ 12, it was Hoyer who dumped a short pass to rookie Trent Taylor, who eluded two Rams and ran the ball to the 1. Instead of pounding it to Hyde again, Shanahan called a play-action pass and Hoyer hit tight end Garrett Celek for a touchdown, cutting LA’s lead to 34-26.

The 49ers later took possession with 6:35 left, and immediately were in scoring position thanks to a 59-yard hookup between Hoyer and Garcon. The Rams’ lead was 41-26 at that point. Shanahan dialed up a handoff to Hyde, then let Hoyer throw it twice. On the second of those, Hoyer checked down to Taylor for a 3-yard touchdown pass.

Here’s how Shanahan explained his conversion from run-only to run-pass: “Everything influences everything throughout the game. Each play matters, how they play stuff. We lost our fullback in the second half, which changes some stuff up, too, the type of runs you can run. When you get into the red zone, especially inside the 5-yard line, there’s lots of fronts and coverages people can play. They can send all-out blitzes and stuff. And if you don’t have a fullback, you’re gonna be outnumbered.”

Fair enough. Juszczyk’s concussion did affect the 49ers’ options. Perhaps Shanahan didn’t make a conscious determination to trust in Hoyer. But when he loosened up his calls, he sharpened his offense.

Hoyer acknowledged as much.

“You’ve gotta do both, just to keep the defense on its toes,” he said. “We also knew that the defense that they play down there was tough to run against. I think that’s part of it. They kind of crowd the box and man everybody up, and they have a lot of people in there to try and stuff the run.”

The 49ers’ late-game heroics, their 19 fourth-quarter points, weren’t enough. Shanahan and Hoyer are still looking for their first win in red-and-gold (or, as they wore for this “Color Rush” game, black and black and black and red). And maybe Hoyer will continue to be good for a crushing interception per game. We all know he’s flawed.

Still, Shanahan has to trust him in pressure situations. Not because he owes it to Hoyer, but because he owes it to his team to be unpredictable.

You can reach columnist Phil Barber at 707-521-5263 or phil.barber@pressdemocrat.com. Follow him on Twitter: @Skinny_Post.

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