Let’s be clear on this. The Giants’ victory over the Patriots Sunday was not one of the biggest upsets in Super Bowl history: It was the biggest Super Bowl upset ever.

The obvious comparison, the Jets’ 16–7 win over the Colts 40 years ago in Super Bowl III, doesn’t really apply here. Back then, AFL and NFL teams didn’t play each other during the regular season, so there was really no way to compare the two teams. In all likelihood, the Jets, given the opportunity to play other NFL teams, would have proven they were clearly the best team in football, or at least that the AFL’s best were better than the NFL’s (a point driven home even more clearly the next year when the Kansas City Chiefs trounced the heavily favored Minnesota Vikings in Super Bowl IV, 23–7).

The only real comparison for a Super Bowl upset of this magnitude is the 2002 game, when Bill Belichick’s Patriots won their first championship against the double-digit-favored St. Louis Rams. In a delicious irony, the latest discovery of the ongoing Spygate investigation, has now called the legitimacy of that game into question. That said, let’s not forget that it was an upset. The gap between the Patriots and Giants was the biggest of any two teams who have ever played in the big one. One number alone suffices to make the point: Prior to Sunday, New England had outscored their 18 opponents by a total of 335 points while the Giants had outscored their 19 opponents by 39 points. You don’t have to be a math whiz to know that outscoring your opponents by 39 points over 19 games is, nine times out of 10, an indication of mediocrity. In fact, over the last half of the season, the Giants were just about a perfect picture of mediocrity. They were 4–4 and outscored in those games by 19 points.

It’s easy now to say that Tom Coughlin and Eli Manning proved their critics wrong, but who could have guessed that this would have happened earlier in the season. For instance, who could have blamed the Giants if they had fired Coughlin after the first two games this year, in which the Giants lost to Green Bay and Dallas by a total of 32 points? At that point in Coughlin’s tenure with the Giants, he had a won-lost record of 25–27, including losses in the only two postseason games he had taken them to.

As for Eli, what was his stock selling for in the 14th game of the season, when they lost to the Redskins, 10–22, and Eli was the 29th ranked quarterback in the NFL? (Even with the strong finish against Buffalo and New England, his NFL ranking was just 25th.) No Giants fan wants to remember it now, but after three full seasons and 14 games into the fourth, Manning’s career was on a road to nowhere, with no indication of greatness to come.

That Eli turned things around can be credited to the real unsung hero of the Giants’ year, quarterbacks coach Chris Palmer. Palmer is a genius at correcting flaws in a passer’s mechanics. He helped send Drew Bledsoe to the Super Bowl in 1997, and the next season, at Jacksonville, he turned Mark Brunell into the highest-rated passer in the AFC. In 2006, working for the Cowboys, he took Tony Romo, a passer who hadn’t thrown a ball in anything but practice in 3 1/2 years, and transformed him into a Pro Bowl selection.

Remember all those slow-motion replays over the previous three years where Manning was clearly throwing off the wrong foot? It took Palmer a few games to work out the kinks, but in the six games from the win over Buffalo through the Super Bowl, Manning threw 10 TD passes with just four interceptions.

The Giants’ other coaching hero, defensive coordinator Steve Spagnuolo, is no longer unsung and unfortunately may not be a Giant for long. The man may be the most creative blitz master since Buddy Ryan with Chicago Bears in the mid-1960s. Spagnuolo’s blitzes didn’t just baffle Tom Brady: They baffled nearly all pro football writers. The postgame congratulations for the Giants defense included many deserved plaudits for their front four, but it was much more than frontline pressure that did Brady in. Watch the game in slow motion, and you’ll see that on nearly two-thirds of the Giants’ blitzes they rushed only five or six men — on a few, they rushed four but held back one of the down linemen for a linebacker or even a safety (Sam Madison was in the Patriots backfield on at least three plays). So baffling was the Giants’ pass rush that in the crucial fourth quarter they had Brady looking for blitzes that the Giants weren’t even sending.

Finally, regarding the issues of whether or not the Patriots’ Super Bowl belly flop diminishes the legacy of Bill Belichick and Tom Brady, and whether it negates the achievement of having gone 18–0, the answers are yes, yes, and yes. Belichick — am I the first to refer to him as Beli-choke? — is now just another coach who has lost in the postseason for three straight years, and this year he lost the big one after bullying his way through the season under a cloud of suspicion for his sleazy spy tactics.

The rap on Brady has been that he has been a good but not great quarterback who has benefited from playing on great teams — a rap which, upon close examination, has a lot of evidence to support it. 2007 is really his only great season, the only time he has led the league in passer rating. He isn’t likely ever to be that good again.

It was Belichick and the Patriots who established the standards by which they must ultimately be judged. They repeatedly ran up scores on beaten opponents for no other reason than to flaunt their domination. The question as to whether winning 18 in a row really means anything now is answered by the T-shirts that can be seen, a day after the game, all over New York: “18–1.” Those are two numbers that, taken together, no New England fan will ever see again without flinching.

Mr. Barra is the author of “The Last Coach: A Life of Paul ‘Bear’ Bryant.”