Norwich were buoyed by their goal and both Adam Drury and Darel Russell came close to doubling their advantage before the interval.
Stockport responded when Michael Rose went on a mazy run before scooping a shot just over the crossbar.
Norwich went two up courtesy of a spot-kick on 69 minutes. Chris Martin went down following a clumsy challenge from Paul Huntington, and up stepped Wes Hoolahan who just beat the outstretched arm of Fon Williams.
Stockport forced a frantic finish when they got one back with nine minutes left, with Carl Baker's shot going in off the backside of the offside-looking Thompson.
However, Holt wrapped up a deserved win with a 90th minute tap-in.