The 37-year-old, sacked and twice intercepted, refused to give in as the Patriots -- at one point down by 10 -- fought their way to a 28-24 victory over the Seattle Seahawks in Glendale, Arizona.
They were helped by one of the less likely calls in football history, as Seattle threw a second consecutive Super Bowl title into the hands of Malcolm Butler.
Patriots rookie Butler made a game-saving interception when the Seahawks, with the ball on the one-yard line and seconds to play, mysteriously chose to pass after an improbable, juggling miracle-catch by Jermaine Kearse.
That moment gave Brady and coach Bill Belichick a fourth Super Bowl victory, a feat matched by only two other quarterbacks: Joe Montana and Terry Bradshaw.
"I just had a vision that I was going to make a big play and it came true," said Butler, 24.
MVP Brady said: "This has been a long journey. I've been at it for 15 years. This one came down to the end and this time, we made the plays.
"Our defense, what can you say about them? Malcolm, what a play. For a rookie to make a play like that and win us the Super Bowl is unbelievable."
Ahead of the game, Belichick had been booed inside Glendale's University of Phoenix Stadium -- the retractable roof, unusually, left open -- as Idina Menzel, the voice of Frozen's Elsa, sang the pre-game national anthem.
Belichick and Brady have denied any wrongdoing regarding the lengthy and unresolved 'deflategate' saga, which concerns underinflated footballs in the AFC Championship game against Indianapolis.
However, Brady was evasive on the subject in a pre-game interview aired on Sunday, and the jeers as Belichick appeared on the big screen made the feelings of many clear.
With that controversy sidelined for the night, the 49th Super Bowl's momentum changed as rapidly as Perry's halftime hits and outfits.
The Patriots had largely outplayed Seattle before the interval, Brady wearing down the Seahawks defense drive by drive.
Brady, in his sixth Super Bowl, found Brandon LaFell for the opening touchdown. In the process, the Patriots left Seattle's famed 'Legion of Boom' verging on bust.
Seattle cornerback Jeremy Lane had already departed the field with an ugly arm injury -- the price he paid for a successful interception -- and, with team-mates Kam Chancellor, Earl Thomas and Richard Sherman all carrying injuries, substitute Tharold Simon became the latest Seahawk on the wrong end of a collision as he failed to stop LaFell.
Seattle quarterback Russell Wilson, essentially anonymous to this point, struck back with the night's first phenomenal pass to 25-year-old rookie and former shoe salesman Chris Matthews.
That allowed the NFL's quiet man -- Marshawn Lynch -- to drive over the line and score.
Patriots tight end Rob Gronkowski mowed down KJ Wright to restore New England's advantage, but that only served to cue up one of the gutsier plays in Super Bowl history.
With seconds remaining in the half, the Seahawks abandoned the safe option of a field goal. Instead, Wilson wasted just 1.79 seconds in delivering a bullet pass down the throat of a jubilant Matthews in the end zone.
Cue Katy Perry, who brought an almost overwhelming array of lights, pyrotechnics and songs to a halftime show she dedicated to her younger self.
Arriving on a giant, mechanical lion before graduating to a shimmy with sharks, Perry opened with Roar before cramming in split-second blasts of Dark Horse, I Kissed a Girl, Teenage Dream and -- lastly -- Firework, during which she ascended aboard a shooting star.
Guest star Missy Elliott emerged to an energetic Get Ur Freak On, relegating the show's other name, Lenny Kravitz, to the background.
When play restarted, Seattle were at the fore.
Having barely seen the ball, that last-gasp score sent the Seahawks into the second half in possession and in control.
The reigning champions immediately moved up by three, Matthews again wrapping up a 45-yard pass play to set up a Seahawks field goal.
After Brady threw his second interception of the night, Seattle wide receiver Doug Baldwin expertly lost New England's Darrelle Revis by running him into an official -- leaving Baldwin all alone in the end zone, and the NFC champions ahead by 10.
Legion of gloom
Brady had been nowhere near perfect but demonstrated his determination as he shrugged off a poor throw, missing Julian Edelman, to find Danny Amendola and get the Patriots rolling again.
Watched by the likes of Paul McCartney, Will Ferrell and Mark Wahlberg, the intensity of New England's offense ground down the depleted Legion as the final minutes ticked away.
With two minutes remaining, Brady once again tried to find Edelman in the end zone. This time he was successful, and the Patriots had overcome a 10-point deficit.
Seattle, however, should have had the last laugh.
Having been granted a near-unbelievable slice of good fortune as the falling Kearse used both knees and a hand to somehow hold on to a pass, the Seahawks made what some observers labelled one of the worst calls in football history.
On the brink of back-to-back Super Bowl victories, Seattle elected to throw the ball, shunning Lynch and gifting Butler the interception.
Following that staggering climax, the game's dying moments descended into a mass brawl which led to the ejection of the Seahawks' Bruce Irvin.
By that point, the fight simply delayed an inevitable New England victory.
"I can't even tell you, I can't even feel it," said Seahawks coach Pete Carroll of the decision to throw the ball.
"For it to come down to a play like that, I hate that we have to live with that."
New England's Edelman said: "We made more plays, we executed when we had to, we have a mentally tough team that works their tails off.
"We are the epitome of what Boston is all about."