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ATLANTA — At long last, it appeared, the losing was over.

And then Nate Clements lost the ball.

A season that's included a pair of punchless losses added its second punch-in-the-gut defeat Sunday as the 49ers lost to the Falcons, 16-14, at the Georgia Dome on Matt Bryant's 43-yard field goal with two seconds left, a boot that gave Atlanta its only lead of the afternoon and was preceded by Clements' soul-crushing fumble.

"We are," said Niners linebacker Patrick Willis, "our own worst enemy."

Indeed, Bryant's game-winner was set up 89 seconds earlier by Clements' apparently game-sealing interception. With San Francisco leading 14-13 and 1:31 left, Clements swooped over the middle to pick off a pass intended for tight end Tony Gonzalez at the Falcons 49 and sprinted down the left sideline.

As Clements ran behind a convoy of blockers, it wasn't clear if he was going to score. But there was little question he had secured the Niners' first win after an 0-3 start — a victory that showed their resilience after the preceding seven days had included a dispiriting 21-point loss, the firing of offensive coordinator Jimmy Raye and the loss of starting safety Michael Lewis, who requested his release Friday.

Instead of overcoming all that adversity, though, they couldn't stand prosperity.

With the ball hanging loosely in left hand, Clements had it punched out from behind at the Atlanta 10-yard line by Falcons wide receiver Roddy White. Falcons offensive lineman Harvey Dahl recovered it at the 7.

Clements exited the locker room quickly after the game and did not speak to reporters.

And Niners coach Mike Singletary, in explaining why he didn't speak to Clements after the fumble, underscored just how painful the miscue was.

"I didn't talk to Nate," Singletary said. "There was nothing to say after that."

Tight end Vernon Davis said he thought the game was over as he watched Clements run free.

"I said that to myself that we got this game," Davis said. "I thought that we had it."

Even after Clements' fumble, the Niners hadn't lost it.

With 82 seconds and three timeouts left, Atlanta still needed to go about 60 yards to get into field-goal range. But their resulting 12-play, 68-yard drive had a certain sense of inevitability as the San Francisco defense, which stayed on the field for 19 consecutive plays in a three-minute, 38-second span, finally wilted.

"It felt like the longest three minutes of my life," Willis said.

With 3:40 left, the Niners had limited the high-powered Falcons (3-1) to 260 yards, 125 below their season average. In addition, quarterback Matt Ryan, after completing 10 of his first 12 passes, had misfired on 6 of his next 16 and White, who had a franchise-record 210 yards against the 49ers last year, had been limited to three catches and 44 yards.

But Ryan and White connected four times for 60 yards in the final four minutes, none more crucial than a 20-yard laser White grabbed in traffic on the right sideline to give the Falcons a first down at the Niners 39 with 52 seconds left.

Linebacker Takeo Spikes conceded the defense was gassed, but still seemed shocked the Niners didn't leave with their first win.

"In my mind, I think the great ones, you've got to be able to overcome it," Spikes said. "It really hurts. I never would have thought this would have happened. The feeling we had before the game. It just felt like it was us against the world."

And San Francisco, hoping to become the second team in NFL history to make the playoffs after an 0-4 start, responded quite well with its backs against the wall.

With new offensive coordinator Mike Johnson calling plays for the first time since a two-game stint seven years ago, the Niners, who hadn't scored a touchdown on their first possession in 19 consecutive games, did just that.

Their 10-play, 88-yard march featured six passes, four runs and a 34-yard pass interference penalty on a third-and-1 at the 49ers 44. Quarterback Alex Smith capped the drive with a 12-yard pass to Davis to give the Niners a 7-0 first-quarter lead.

With their play-calling seemingly in better hands, the 4ers received more heartening news less than two minutes later.

On fourth down at Atlanta's 12, Dominique Zeigler flew through the middle to block Michael Koenen's punt. The ball caromed into the end zone and rookie safety Taylor Mays, tiptoeing on the end line, made an athletic move to stay in bounds and grab the ball, giving the Niners a 14-0 lead and their first touchdown off a blocked punt in 23 years.

Mays, making his first career start in place of the absent Lewis, continued his strong performance, finishing with a team-high 11 tackles.

The offense, on the other hand, never scored again — or ventured inside the Falcons 34-yard line — on its final seven drives, which ended with five punts and two interceptions from Smith.

Singletary said he thought Smith, who completed 21 of 32 passes for 188 yards, "played well for the most part." But Smith had a harsher assessment, saying his picks were just as critical as Clements' fumble.

"In the end," he said, "you look back and see it cost us the game."

Leading 14-7 at Atlanta's 34 with 1:20 left in the second quarter, Smith, under pressure, threw a high pass which caromed off running back Frank Gore's hands and was picked off by Falcons linebacker Curtis Lofton. Atlanta turned the miscue into Bryant's 37-yard field goal and trailed 14-10 at halftime.

On the 49ers' first possession of the second half, their promising 10-play, 38-yard drive ended when Smith's pass intended for Josh Morgan was intercepted by safety William Moore at the at Falcons 33 and returned 13 yards, leading to another field goal.

Despite those turnovers, the 49ers were still in position to grab their first win.

In the end, though, they couldn't overcome one more critical mistake.

"The day we can find out how to overcome ourselves, will be the day we turn this around," Willis said. "We've just got to find a way to stop killing ourselves."

For more on the 49ers, go to Instant 49ers at blog.pressdemocrat.com/49ers. You can reach Staff Writer Eric Branch at eric.branch@pressdemocrat.com and follow him at twitter.com/Eric_Branch.