The honours looked set to be shared at Glanford Park until hitman Holt struck at the death with a fine header to secure the points for Paul Lambert's men.
Scunthorpe had won 2-1 at Reading on the opening day and then beaten Oldham in the Carling Cup in midweek, yet Holt's predatory instincts put paid to their hopes of a third successive win.
The Canaries almost led inside the third minute when an outswinging corner from midfielder Andrew Surnam was greeted by a firm header by Andrew Crofts from 12 yards.
The ball flashed just wide and the hosts survived but Norwich continued to probe and defender Adam Drury drilled a left-footed shot wide from distance in the ninth minute.
Moments later, Scunthorpe midfielder Martyn Woolford hit a fierce shot from 25 yards which drew a fine block from Canaries defender Michael Nelson.
In the 24th minute, Josh Wright carved out a chance for Scunthorpe when he crossed dangerously for a header which Jonathan Forte headed goalwards.
Canaries goalkeeper John Ruddy made a fine parried save to prevent a certain goal and Scunthorpe cleared the danger with a fine defensive header.
In the 34th minute, Woolford engineered the space to a drill a shot goalwards from 20 yards but Ruddy made a comfortable save.
The momentum remained with the home side as the interval approached and summer signing Chris Dagnall narrowly failed to hit the target from 18 yards in the 36th minute.
In the 40th minute, Scunthorpe went close again when a cross from defender Eddie Nolan was volleyed over the crossbar by Forte.
The lively Forte went close again before half-time with another snapshot but genuine chances remained scarce in the opening period.
The Iron looked to up the tempo after the restart as midfielder Garry Thompson hit a shot from 25 yards which drew another fine block from Nelson.
In the 53rd minute, Holt missed the target from 12 yards and playmaker Wes Hoolahan also went close for the visitors.
Substitute Andrew Wright went close for Scunthorpe with a 30-yard in the 77th minute but it was an hopeful effort and did not trouble Ruddy in the visitors' goal.
With eight minutes remaining, Simeon Jackson engineered the space to hit a shot from the edge of the box which again missed the target.
However, in the first minute of added time Surman crossed from the left flank and Holt rose highest to head home the winner.
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