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Former England manager Graham Taylor, who supported them as a boy on the terraces at the Old Showground, was back at the club for the first time as a vice-president to see skipper Andrew Crosby lift the trophy.
In the early stages it was League One's 32-goal leading marksman Billy Sharp - he was presented with the Golden Boot before the match - who caused all sorts of problems to the Carlisle defence.
But for once he could not find his finishing touch, twice pulling efforts just wide of the target.
In a feisty affair winger Cleveland Taylor finally made the breakthrough in the 41st minute with the first goal he has scored at home all season.
He forced a close-range shot under the body of goalkeeper Keiren Westwood to start the champagne celebrations.
Striker Kevin Gall almost equalised for the visitors with an angled drive that brought the best out of goalkeeper Joe Murphy.
Taylor almost made it 2-0 on the stroke of half-time with a shot that was cleared off the line by full-back David Raven.
Scunthorpe increased their lead in the 47th minute with a fierce shot from midfield man Matthew Sparrow.
The opening was created by a good knock-down in the box by veteran targetman Steve Torpey who was making his last appearance for the club after seven years.
Torpey was replaced on the hour by substitute Jermaine Beckford who made it 3-0 with almost his first touch when he squeezed a shot home at the near post.
As Torpey left the pitch - via embraces with several team-mates - he was given a rousing standing ovation by the home fans.
In the closing stages Carlisle were denied again by a good save from Murphy to keep out another effort from Gall.
The final whistle triggered scenes of wild jubilation from the Scunthorpe fans as manager Nigel Adkins saluted his side.
United were presented with the League One trophy after the match, and spent more than an hour on the pitch celebrating with fans.