Ahmad Bradshaw scored on a six-yard touchdown run with 57 seconds remaining to lift the Giants to a 21-17 win on Sunday.
Manning led the 88-yard drive to win the game and was named Most Valuable Player, just like he orchestrated an 83-yard drive to capture the 2008 Super Bowl over the Patriots, which ended New England's hopes of a perfect season and ended with Manning winning MVP.
With time running down -- and a chance to let it tick off even further -- Bradshaw nearly sat at the half-yard line before falling back into the end zone for the touchdown. A two-point conversion failed.
Tom Brady completed a 19-yard pass to Deion Branch on 4th-and-16, but a last- second Hail Mary pass fell incomplete in the end zone, just out of the reach of injured tight end Rob Gronkowski.
Just as New York's winning drive four years ago had an instant-classic play, this one got its goosebumps moment with 3:39 remaining.
It was Mario Manningham's 38-yard catch near the left sideline on the first play of the drive, which took the Giants to midfield. Manningham got behind cornerback Sterling Moore, and took a hit from safety Patrick Chung, but kept his feet in bounds for the catch.
The play was upheld upon review, with Manningham scraping his back foot on the turf before he tumbled head-first out of bounds.
Manning was 5-of-6 for 74 yards on the drive and passed big brother Peyton by winning his second Super Bowl ring. He finished the game 30-of-40 for 296 yards and a touchdown pass to Victor Cruz in the first quarter.
Brady set a Super Bowl record by completing 16 straight passes and ended 27- of-41 for 276 yards with touchdown passes to Danny Woodhead and Aaron Hernandez.
But Brady failed in his attempt to win four titles in the last 11 seasons and match his idol, Joe Montana, and Terry Bradshaw with four Super Bowl wins as a quarterback.
The Giants won Super Bowl XLII, 17-14, four years ago after a final drive that included David Tyree's now-famous helmet catch and Plaxico Burress' 13-yard touchdown reception with 35 seconds remaining.
Their win Sunday in Super Bowl XLVI capped an improbable run that almost never happened. New York only made the playoffs by beating Dallas in the last game of the regular season.
Of course, the regular season also included a 24-20 win over New England in Week 9. The Patriots won 10 straight games in between that loss on November 6 and Sunday's Super Bowl.
Brady set a Super Bowl record for consecutive completions and threw a 12-yard touchdown pass to Aaron Hernandez that helped the Patriots take a 17-15 lead over the Giants after three quarters.
Brady's 16th straight completion going back to the first half found Hernandez across the middle and the second-year tight end broke a tackle by safety Deon Grant to get into the end zone.
After completing his final 11 passes in the first half -- including 10 on a 96-yard touchdown drive that tied a Super Bowl record -- Brady was 5-for-5 on the 79-yard drive that opened the third quarter.
Brady's 16 straight completions tied his own postseason record and broke the Super Bowl record of his idol, Joe Montana, during Super Bowl XXIV in 1990. Brady's 16 postseason wins are tied with Montana for most playoffs victories by a quarterback in NFL history.
The Giants responded to Hernandez's touchdown with a 45-yard drive that ended in a 38-yard field goal by Lawrence Tynes to get them within 17-12. The drive was set up by Jerrel Jernigan's 34-yard kickoff return.
New England went 3-and-out after that, with Giants defensive end Justin Tuck sacking Brady on third down and driving the quarterback's left shoulder into the turf.
New York, with good field position at the Patriots 48, turned around and kicked another field goal to get within 17-15. Tynes was good on the 33- yarder.
Soon after, the Giants couldn't cashed in a turnover for points.
Brady was being pursued by three Giants defenders when he heaved a pass downfield for Gronkowski as Jason Pierre-Paul delivered a hit. In coverage in front of Gronkowski, linebacker Chase Blackburn intercepted what was basically a jump ball at the Giants eight-yard line.
The ensuing Giants drive ended in a punt after Manning's third down pass to Manningham fell incomplete. Cornerback Sterling Moore made contact with Manningham from behind as the pass was being broken up and New York coach Tom Coughlin was seen screaming on the sideline.
Earlier, Brady threw a four-yard touchdown pass to Danny Woodhead to cap a Super Bowl record-tying 96-yard drive near the end of the second quarter and give the Patriots a 10-9 lead going into halftime.
Brady was 10-for-10 on the drive and completed his last 11 passes in the half. The 96-yard drive came after the Patriots were pinned in deep by a punt.
In fact, Manning started the game 9-for-9 and threw a two-yard touchdown pass to Victor Cruz to give New York a 9-0 lead after the first quarter.
New York also got two points on a safety when Brady was called for intentional grounding on New England's first play from scrimmage.
Brady's pass, under pressure, was thrown 45 yards downfield from the front of the end zone with no receiver in the vicinity and was the sixth safety in Super Bowl history.
Manning led the Giants on a 78-yard drive after that, which included a penalty on New England for too many men on the field that reversed a fumble by Cruz.
The drive was capped by Manning's short pass to Cruz behind two defenders with 3:24 left in the quarter, making it 9-0.
The Giants ran 19 of the game's first 20 plays from scrimmage as New England had trouble getting out of its own way early.
But the Patriots started a 60-yard drive that spanned the first and second quarters and ended in Stephen Gostkowski's 29-yard field goal, pulling them within 9-3.