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SANTA CLARA — With a few seconds left in the 49ers’ first win of the season and their first win of the Kyle Shanahan Era, a 31-21 victory against the New York Giants, general manager John Lynch was on the sideline hugging players.

Players were on the sideline hugging Shanahan. Waiting in line to hug him. Even Lynch waited in line. Eric Reid cut to the front and poured water on Shanahan’s head. And as Shanahan walked across the field after the game, he playfully punched the 49ers PR director in the shoulder, as if to say, “We won!”

Shanahan was in love with everyone and everyone was in love with him.

“When you lose nine in a row, you learn to savor the moments and enjoy these,” Shanahan said at his postgame press conference. “It was tough work for us to get our first win, and we got it. I think the guys knew how much it meant to me, and I knew how much it meant to them.”

Center Daniel Kilgore knows exactly how much the win meant to Shanahan.

“We don’t expect outsiders to understand,” Kilgore said at his locker after the game. “They think they know, but they don’t know. (Shanahan) has been a part of a lot of teams, a lot of wins, some great wins, some bad losses. For him to have his first win as the 49ers head coach, it’s special. Growing up in the Bay Area, his father coached here — it’s huge.”

As Shanahan walked off the field toward the locker room, defensive end Elvis Dumervil grabbed Shanahan and lifted him off his feet.

“We believe in you, Coach,” Dumervil told Shanahan. “It hasn’t gone the way we want it to, but we know we’re heading in the right direction.”

Granted, the 49ers were playing a bad Giants team that has won only one game this year. But the 49ers played a clean, efficient, smart game. They didn’t drop any passes, they committed only six penalties and they were balanced on offense.

Last week against the Cardinals, Shanahan called 57 passes and 16 runs, Against the Giants, he called 25 passes and 33 runs. Balance.

Running back Carlos Hyde carried the ball 17 times for 98 yards. Backup running back Matt Breida carried the ball nine times for 55 yards, including 33-yard touchdown run that put away the game.

“It was an outside zone play,” Breida said. “The offensive line and receivers did a great job of blocking. I saw the cutback and there was no one back there. I hit the hole, and I ran to the touchdown.”

The 49ers’ commitment to their run game helped protect quarterback C.J. Beathard, who took 15 hits and five sacks last week. Against the Giants, he took just two hits and no sacks.

For the first time this season, Beathard wasn’t under constant pressure. And he played well. He completed 19 of 25 passes, threw two touchdowns, ran for one and posted a quarterback rating of 123.4. That was the third-highest passer rating by a starting quarterback this week, behind Tom Brady of the New England Patriots and Jared Goff of the L.A. Rams.

“There’s really not a better feeling,” Beathard said after the game. “It’s been a long time coming. We’ve been so close for so many games. It’s a play here, a play there that can change the whole course of a game.”

Beathard’s best play was an 83-yard touchdown pass to Marquise Goodwin. But Beathard’s most vital contribution may have come on third downs.

Entering the game, the 49ers had the third-worst third-down offense in the league, converting just 31.6 percent of the time. Against the Giants, the 49ers converted eight-of-12 third downs – 66.7 percent.

“To be able to make those third downs,” Shanahan said, “to stay on the field, to allow you to run your offense, mix in the run game a lot, have some play actions, some keepers off of it, not having to drop back very much — it takes the pressure off everybody. Mainly the quarterback, but also the O-Line, the receivers, the backs. You make them defend the whole field (the opponent) and you put guys in more of an advantageous (position).”

As well as the offense performed, the defense played maybe better.

After it gave up two field goals during the first quarter and a touchdown with 2:13 left in the second quarter, the 49ers defense held the Giants offense scoreless until late in the fourth quarter when there was 1:07 left in the game. By then, the 49ers were winning 31-13, and the game essentially was over. It was garbage time.

“That was just one win, but it definitely felt good and we worked hard for it,” Shanahan said. “I got that monkey off my back. Now I have to get my second one, or that will eventually be a monkey too.”

The second monkey comes later. On Sunday, it was time to celebrate, finally.

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