SAN JOSE — It can be hard to make history at Serra.

The San Mateo school is famously excellent across a variety of sports. But it had been a while since the Padres won a Central Coast Section baseball championship.

Not anymore. Facing a two-run deficit in the early innings, top-seeded Serra rallied for three runs in the fourth, and the Padres’ pitching held the line to secure a 3-2 win over second-seeded Valley Christian and their first Division I championship since 2009.

The Padres are most famously the school that raised Barry Bonds and Tom Brady. But that undersells the Serra baseball program’s sustained greatness.

Serra (26-6) has now won seven section championships, including three of four from 1993-96, and finished as runner-up six other times. Now, the Padres are back on top and back on the map.

“Nobody expected it from this team after graduating 18 seniors last year, but it was something that fueled us all season,” second-year Serra coach Mat Keplinger said. “We knew we were a talented club, and for them to come together, especially these seniors, the two-year run that they’ve had, the work ethic, changing the culture of the program, their legacy is going to going to last for a long time, and I’m going to miss the heck out of these guys.”

Valley Christian (25-7-1) was the early aggressor on Saturday night. The Warriors took the initial lead in the first inning when Brock Ketelsen led off with a single and scored on a safety squeeze by Jordan Ortiz.

The Warriors doubled their advantage in the third. Kelan Cunningham led off with a single and Quinten Marsh scored him with a single to right.

Serra had a quick and lasting rebuttal in the fourth. Jack Armstrong got things going with a leadoff single, then Tyler Harrison drew a walk.

Aaron Minton then came through with the biggest hit of the game, a frozen-rope double down the left field line that scored both baserunners and tied the game 2-2.

Serra took the lead when Evan Bradshaw’s infield single scored Minton later in the inning.

“It’s a resilient group, and they believe in themselves,” Keplinger said. “They play for each other, and it continues to show.”

When Serra’s offense came through in the fourth, the Padres’ pitchers suddenly had a lot more to work with.

Riley Lim, who started the game, pitched a clean fifth to give Serra a shutdown inning. Then Nate Hui took over, finishing the game with two shutout frames.

Valley pressured Serra all the way to the bitter end. In the seventh, Ethan Flynn, the tying run who had reached base on a walk, advanced to third on a passed ball with Ketelsen, the winning run, also on base. At that point, VC coach John Diatte pushed his chips in.

Diatte called for another safety squeeze, but this time, Serra was ready. Hui fielded the bunt attempt from Narvaez and flipped the ball to home plate backhanded, beating Flynn in plenty of time.

With two outs, Hui committed a balk while facing Quinten Marsh, moving Ketelsen and Navarez to second and third.

But amid the chaos — some self-created — Hui came through. He struck out Marsh and his .518 batting average looking on an outside breaking ball, securing the section title for Serra.

“He’s pitching in the biggest moments, and he’s made it interesting a lot of those outings. That’s when he thrives. He’s done it all year,” Keplinger said of Hui. “Somehow, someway, we get the best hitter to the plate with the game on the line. Nate has been in those moments, and championships are supposed to be hard to win. We earned it.”