Brees capped his record-setting season by throwing for 462 yards and four touchdowns, throwing two go-ahead strikes in the final 5 minutes only to see the 49ers rally for a 36-32 playoff victory Saturday.
"It stings right now because of the expectation level that we had coming into this tournament and understanding that if we win here we're into the NFC championship game and anything can happen," Brees said. "That's tough. Tough to swallow at this point."
But the defense failed to close it out, allowing the 14-yard game-winner from Smith to Vernon Davis with just 9 seconds to go for San Francisco (14-3).
"There is a finality to the playoffs," Brees said. "You go from thinking of the NFC championship to all of a sudden you're going home and there's no more football until next year."
All those passing records Brees set turned out to mean nothing. Brees shattered Dan Marino's 27-year-old mark of 5,084 yards passing by throwing for 5,476. He had 468 completions this season, breaking Peyton Manning's 2010 mark of 450. He finished the season completing 71.6 percent of his passes, breaking his own 2009 NFL record of a 70.6 completion percentage.
He followed that up with 466 yards passing in a first-round win over Detroit and then a record-setting 40 completions in a losing cause against the 49ers. Brees has had the top two regulation playoff games in NFL history the past two games.
"They ended up making one more play than we did tonight," coach Sean Payton said. "I was proud of how we fought. I was proud of our guys despite some of the early adversary - the turnovers."
The Saints committed four first-half turnovers starting with running back Pierre Thomas getting knocked out by Donte Whitner on a hard hit near the goal line before fumbling on the opening drive. Brees then threw a pair of uncharacteristic interceptions, the first ending a record streak of 226 straight postseason passes without one.
Sproles took a short pass from Brees and sprinted down the field for his score that made it 24-23. But the oft-maligned Smith, whom most 49ers fans did not want back in San Francisco this season, delivered in the clutch.
He fooled the Saints on his 28-yard touchdown run around left end to put San Francisco back ahead. But Brees answered quickly, threading a perfect pass to Graham that beat Patrick Willis and Whitner to put the Saints ahead 32-29 on a 2-point conversion with thoughts of going to a third NFC title game in six seasons.
"I think we got too excited," Sproles said. "We didn't think they could score like that, but they did. They proved I was wrong."
Smith completed five passes for 85 yards, mixing a couple of dumpoffs to Frank Gore with a pretty 47-yarder to Davis down the left sideline. Then with the Saints needing just one more stop to force the 49ers into a game-tying field goal attempt, Davis got inside of safety Roman Harper for the game-winner, absorbing a hard hit from the safety to make the catch in the opposite end zone from where Dwight Clark made "The Catch" 30 years ago to start the 49ers dynasty.
"That is not our style of defense," safety Malcolm Jones said. "We don't play prevent, we have never played it, and nothing is new. Nothing has changed so we live by the blitz and we die by the blitz."
Davis, who wept on the sideline afterward days after saying he was overwhelmed early by Harbaugh's thick playbook, finished with seven catches for 180 yards. It was the most yards receiving by a tight end in a playoff game.
Smith went 24 for 42 for 299 yards with three TD passes and the touchdown run. He also helped the Niners become the first team in NFL history to score two lead-changing touchdowns in the final 3 minutes to win a playoff game, according to STATS LLC.
"Guys were so confident, as long as we had time we had a shot," Smith said.
Notes: Sproles had a playoff-record 15 catches for 119 yards. ... The Saints had lost five fumbles all season, then gave three away against San Francisco. ... Brees finished the regular season and playoffs with 6,404 yards passing, surpassing Marino's 6,085 on the way to the Super Bowl in the 1984 season. ... The Saints converted an NFL-record 56.7 percent of their third downs in the regular season but just 5 of 14 this game.