Syracuse emerged with the victory when Syracuse's Hakim Warrick blocked a potential three-point shot by Michael Lee with 1.5 seconds remaining, after which Kansas star Kirk Hinrich had a three-point effort sailed wide at the buzzer.
"I am happy, but I am truly happy for our fans," Boeheim said. "We played the best first half we could play and then just had to hang on.
"You have to credit Kansas. They really fought back. But our kids would not give up against a great Kansas team."
The Orangemen stormed to an 18-point lead during the first half with McNamara making six of his team's 10 three-point shots during the period.
Kansas then put together a 10-point run early in the second half to make a game of it, but the Jayhawks' bid for a national championship began to fade in a series of missed opportunities and woeful free-throw shooting.
Three times during the middle portion of the second half, the Jayhawks had the ball while trailing by just three points.
But on each occasion, Kansas turned the ball over. And when the Jayhawks missed eight straight free throws as part of a 12 of 30 performance from the line, their hopes were all but wiped out.
Kansas, however, made a final charge and got to within two points with 57 seconds to go on one of two free throws by Jeff Graves.
Kueth Duany then made one of two for Syracuse for an 81-78 advantage with 24.1 seconds to go. Hinrich had a chance to tie it, but his three-point attempt rattled in and out with 16 seconds to go.
Warrick was fouled for Syracuse and one free throw would have virtually clinched the game, but he missed two tries from the line, giving Kansas a final opportunity.
Lee's attempt from the corner, however, was swatted out of bounds by Warrick and Hinrich missed yet again.
McNamara's three-point barrage allowed him to steal some of the spotlight from fellow freshman Carmelo Anthony, who led the Orangemen with 20 points. Anthony, playing with a sore back, was named the tournament's Most Outstanding Player.
McNamara, who led Syracuse to a 10-of-13 effort from long range in the first half, did not produce a point in the second half and finished with 18.
Kansas was led by Keith Langford with 19 points, but he fouled out with more than five minutes remaining. The Jayhawks' senior star twosome of Nick Collison and Hinrich combined to score 35 points.
Syracuse became NCAA champions with a 30-5 record and allowed Boeheim to gain at least some measure of revenge for the most disappointing night of his coaching life.
On this same Louisiana Superdome court 16 years ago, Boeheim's Orangemen were beaten in the title game by Indiana on a shot in the final seconds by Keith Smart.
"I think this building owed me one," Boeheim said. "After the game, I told Roy the same thing (then Indiana Coach) Bobby Knight told me that night. I told him he will be back."
This was Boeheim's third trip to the Final Four his 37 previous tournament victories were the most ever by a coach without a national championship to his credit.
McNamara and Anthony both made a three-pointer in the opening six minutes of the game, but Syracuse held only a 10-8 advantage when Collison made a three-point play.
Kansas then went more than 11 minutes without scoring more than two points in a row.
During that stretch, the Orangemen consistently fell back on defense in rapid style to prevent Kansas from getting its normally dominating fast break working. And when Kansas settled into its half-court offense, Syracuse used the kind of quickness that made it seem as if it had eight men on the floor.
McNamara, meanwhile, picked his spots to throw daggers into the Kansas hopes. He hit two three-pointers in a row inside the 13-minute mark that boosted Syracuse's lead to 23-14. Another long-range shot fell in with eight minutes to go in the half for a 37-23 advantage and he made the advantage 42-27 with yet another.
The Syracuse lead grew to 18 with four minutes remaining in the half on a three-point shot by Duany, but Kansas finally came to life with an eight-point run that cut the deficit to 47-37 with 2:18 remaining.
The Jayhawks then appeared to have taken another bit out of their deficit when Aaron Miles knifed into the lane and tossed up a floater that went in. Just as he released the ball, Miles collided with McNamara and it seemed as if McNamara was moving into Miles.
But charging was called on Miles, negating the basket. Seconds later, Kansas players complaining on the sidelines, McNamara hit his sixth three-pointer of the half.