Restored to the starting lineup, the Canaries skipper proved the difference as a hectic second half at Carrow Road saw Dan Gosling sent off for Alan Pardew's men.
Wes Hoolahan bundled the opener over the line from a disputed corner in the first half before Demba Ba broke through the defense to equalize on the stroke of halftime.
Norwich then hit Newcastle with a four-minute double blow, with Holt regaining the lead through a header on the second attempt before Steve Morison arrived to dispatch the third, also with a fine headed effort.
Dan Gosling was sent off for the visiting side when he was adjudged to have committed serious foul play on Russell Martin and, despite Ba raising Newcastle's hopes with a well-taken second moments later, Holt put the result beyond doubt with another excellent aerial goal.
With Newcastle missing first choice center backs Steven Taylor and Fabricio Coloccini, Paul Lambert elected to recall super sub Holt to the starting XI alongside Steve Morison, with Wes Hoolahan also coming in as one of four changes to head a midfield diamond. For the visiting side, right back Danny Simpson was called on to fill in in the center alongside the inexperienced James Perch, with Shola Ameobi preferred up front to Hatem Ben Arfa.
With 20 minutes on the clock, Holt did the hard work in bullying his way past Perch and into the area, but his angle coming in from the right meant that he had to shoot with his unfavored left foot and his effort was easily blocked by Simpson.
As the match approached the half hour point, there were deafening shouts for handball as Davide Santon appeared to take a cross from the right onto his left forearm in the area, but referee Martin Atkinson ignored the vociferous appeals.
A corner would lead to the opening goal. An almighty scramble came from it in which Tim Krul saved from Andrew Crofts' header before Hoolahan got the last touch in bundling the ball over the line.
A very simple goal then got things back to level terms on the stroke of halftime. Hanging around in front of the assembled Norwich back four, Yohan Cabaye knocked an elegant ball over the top and Ba broke the offside trap to find himself one-on-one with John Ruddy in the kind of chance he does not make a habit of missing.
Despite the first 15 minutes of the second half being dominated by a superior-looking Newcastle, it was the Canaries who took back the lead. David Fox's corner came back to him, and he used the second ball to launch it towards Holt. The captain's first header was blocked but he was able to take another bite and this time saw it drop into the net off the underside of the bar.
Barely a moment later Norwich had another, Holt tussling for the ball on the edge of the area and ensuring that the ball was distributed to Crofts on the right, where had all the space he could need to line up a cross. Morison, who had previously had a very quiet game indeed, rushed onto it to extend his excellent scoring form with a bullet header.
Things then went from bad to worse for the visiting side when Gosling clattered viciously into Russell Martin, appearing to both tread on him and catch him with his shoulder, earning himself a straight red card.
The Magpies found a reply when Ameobi was allowed to wriggle free of his marker on the right and delivered a sumptuous through ball to put Ba into the danger area. The Senegalese took Martin out of the equation with a delightful first touch before burying his second of the afternoon into the bottom corner.
Lambert moved to close the game out by introducing Bradley Johnson, and he contributed immediately by delivering a fine free kick into the crowded area, where Holt was waiting to stoop low and power a fine header into the top corner.