The Patriots are being investigated over allegations they under-inflated balls in beating the Indianapolis Colts to reach the showpiece event.
But, despite trailing 24-14, they rallied to become the first team in Super Bowl history to trail by double digits in the second half and win.
The Patriots took the lead with two minutes left and held on for victory.
The New England Patriots quarterback Tom Brady was named the most valuable player of Sunday's Super Bowl, with the 37-year-old throwing four touchdown passes, including two in the fourth quarter.
He set a new record for career Super Bowl touchdown passes with 13 to break the old mark held by his childhood idol Joe Montana. Brady's 37 completions also set a new Super Bowl record.
Pop star Katy Perry was the star attraction at the interval and she was joined by special guests Lenny Kravitz and Missy Elliott.
Perry entered the pitch on a giant golden robotic lion as she sang her hit 'Roar' before Kravitz provided some rock and Missy Elliott some hip-hop.
The climax saw Perry lifted 50 feet off the ground by a mechanical contraption and she sang 'Firework' as she floated above the pitch.
Seattle Seahawks head coach Pete Carroll was criticised for his decision to throw, rather than run the ball with powerhouse Marshawn Lynch, with his team a yard out and just seconds remaining.
"That play call will haunt Pete for the rest of his career," said former Cowboys receiver Terrell Owens.
"Why get cute at that point?" ex-Green Bay Packers player Bucky Brooks commented.
However, Katy Perry received some praise. Pop star Britney Spears said: "That half-time show! Katy Perry you rocked it."
The New England Patriots overcame the 'deflate-gate' row to beat the Seattle Seahawks 28-24 in the Super Bowl.