ATLANTA — Everything was going wrong for the San Francisco 49ers and their proud defense.

Julio Jones and the Atlanta Falcons gouged them so often in the early stages of the NFC title game that the 49ers seemed too stunned to respond.

“It was us, it wasn’t them at all,” San Francisco linebacker NaVorro Bowman said. “We weren’t communicating, playing the way we want to play. We regrouped in the second half and played our game.”

They certainly did.

Bowman, Patrick Willis and Ahmad Brooks combined to stop the Falcons 10 yards short of the end zone in the closing minutes of a 28-24 victory Sunday that sent San Francisco to the Super Bowl for the first time since 1995.

After Bowman essentially sealed the game by breaking up a fourth-down pass from Matt Ryan to Roddy White with 1:09 remaining, the Falcons had time to run just one more desperate play before the buzzer sounded.

It was yet another big play for a defense that clamped down on Ryan and Atlanta’s high-powered passing attack over the final 30 minutes.

“They’ve got some horses, man,” San Francisco defensive tackle Justin Smith said. “They made it tough on us. We made some adjustments at half, played a little bit better, but our offense picked up a lot of slack today, kept us rolling, kept us in it and we were able to win it.”

The Falcons got off to a dominant start as Ryan and Julio Jones combined for a pair of touchdowns that helped make it 17-0 early in the second quarter and 24-14 at halftime.

But midway through the third, cornerback Chris Culliver intercepted a pass at the San Francisco 38 that allowed the defense to build confidence.

Though the Niners’ offense failed to score off the turnover when David Akers missed a 38-yard field goal attempt, defensive end Aldon Smith followed on the next defensive series by recovering Ryan’s fumble on a botched shotgun snap.

The offense again failed to score when receiver Michael Crabtree lost a fumble at the Atlanta 1, but after forcing the Falcons to an ensuing three-and-out, the defense was delighted to see Frank Gore run for a 9-yard touchdown and a 28-24 lead.

“We believe in our offense,” Willis said. “We understand that if we get stops, they’re going to score points.”

The turn of events contrasted sharply from the early stages of the game when the 49ers appeared to have no answer for Ryan, White, Jones and Tony Gonzalez.

By the first minute of the second quarter, Jones had scored two TDs, beating cornerback Tarell Brown both times. On the first score, it seemed that Brown mistakenly released Jones on a deep route, and the blown coverage allowed Jones to outrun free safety Dashon Goldson for a 46-yard score.

After Falcons kicker Matt Bryant’s 35-yard field goal made it 10-0 on Atlanta’s second possession, Ryan and Jones hooked up on a 20-yard TD. Jones caught the ball over his right shoulder in the left back corner of the end zone and deftly kept both feet inbounds to make it 17-0.

Jones and White combined for 226 yards receiving on 13 catches in the first half, many of them coming on underneath crossing routes as the two wideouts made several athletic plays.

In the second half, however, Jones and White combined for six catches and 62 yards.

Good fortune helped the Niners rally, too.

On the Falcons’ final drive, cornerback Carlos Rogers fell down while covering slot receiver Harry Douglas on a deep pass near the right sideline, but San Francisco caught a big break when Douglas stumbled on his way to making a disputed 22-yard catch at the Niners 28.

Had he stayed on his feet, Douglas could have scored a touchdown on Atlanta’s final drive.

“It made it tough on them,” Rogers said. “Things like that happen. No excuses. We made the plays and were able to get off the field.”

Such was the case throughout the regular season as the Niners ranked among the top four in scoring average, third-down efficiency, yards rushing and yards passing.

They just needed to reclaim their identity and prove they had moved past the disappointment of last year’s NFC title game loss to the New York Giants.

“I don’t really think it’s destiny or anything like that written on the walls,” Smith said. “It’s the team that works the hardest, prepares the hardest and has the best players and coaching staff. You pour all that in together and it comes out pretty good at the end.”

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