49ers punt returner Kyle Williams fumbled twice in the game, directly leading to 10 Giants points, including the game-winning field goal.
The Giants will play the New England Patriots in Super Bowl XLVI, after the Patriots beat Baltimore 23-20.
Williams fumbled in overtime to set up Lawrence Tynes' 31-yard field goal, and the 49ers lost the NFC championship game to the New York Giants 20-17 on Sunday.
Williams, returning kicks in place of the injured Ted Ginn Jr., muffed one punt early in the fourth quarter to set up a go-ahead touchdown for New York, then was stripped by Jacquian Williams in overtime to give the Giants the ball at the 24.
After three runs and a kneeldown, Tynes kicked the game-winner, and Williams slowly made a dejected walk back to the locker room as the 49ers missed out on a prime chance to go to the Super Bowl.
The fact that turnovers did in San Francisco was truly surprising. The 49ers tied an NFL record with just 10 giveaways all season -- including none on special teams -- and had a plus-28 turnover margin in the regular season. They took advantage of five New Orleans turnovers to win 36-32 last week but were on the wrong end in this game because of Williams.
Williams, the son of Chicago White Sox general manager Ken Williams, did not look smooth fielding punts after doing it just twice in the regular season.
He made a dangerous, sliding catch on one return and called a fair catch on another with room to run. He then made his first big miscue after San Francisco forced a punt early in the fourth quarter while protecting a 14-10 lead.
Steve Weatherford hit a short, bouncing punt that Williams came up to try to field. He backed away at the last minute, but the ball glanced off his right knee and was recovered by Devin Thomas at the San Francisco 29. The play was originally not ruled a fumble but was overturned by instant replay.
Six plays later, Eli Manning threw a 17-yard touchdown pass to Mario Manningham, who beat backup cornerback Tramaine Brock on third-and-15. Brock was playing in place of starter Tarell Brown, who left late in the third quarter after a violent collision with teammate Dashon Goldson.
Williams helped atone for his miscue when he returned the kickoff 40 yards to help set up David Akers' tying field goal late in regulation.
But on his second return in overtime, Williams gave the ball away again. He fielded the punt at the 19 and was stripped by Jacquian Williams. Thomas once again pounced on the ball at the 24, setting up the Giants' winning kick and ending San Francisco's most successful season in years.
Coach Jim Harbaugh got the Niners to the brink of the Super Bowl in his first season, taking over a 6-10 team and going 13-3 to win the NFC West. The ability to protect the ball and cause turnovers was the biggest reason for the turnaround.
But the Niners forced no turnovers by the Giants and were done in by Williams' costly giveaways.
The Niners really did miss Ginn, who injured his right knee in last week's thrilling 36-32 win over New Orleans. San Francisco was already thin at receiver after releasing Braylon Edwards late in the regular season and was unable to get anything out of its wideouts this game.
San Francisco's wide receivers had just one catch all game -- a 3-yarder by Michael Crabtree on a third-and-5 play before Akers' tying field goal with 5:39 left in regulation.
The bulk of San Francisco's offense came on two big passes from Alex Smith to Vernon Davis. They connected on a 73-yarder to open the scoring in the first quarter and a 28-yarder to take a 14-10 lead in the third.
The Associated Press contributed to this report