The home side ultimately ran out comfortable winners, but often made hard work in disposing of Stockport, who played two thirds of the match with ten men following the 29th minute dismissal of central defender Michael Raynes for a foul on Marc Tierney.
By that time Shrewsbury had taken the lead through fit-again striker Andy Cooke - starting his first game since the opening day of the season - but a spirited Hatters comeback saw them draw level on 74 minutes with a fine Anthony Pilkington goal.
Their joy, however, was short-lived as Ben Davies scored for the third successive game to restore Shrewsbury's lead, with the outcome put beyond all doubt with a Dave Hibbert penalty four minutes from time.
When the teams met back on New Year's Day Shrewsbury had run out 4-2 winners with Cooke grabbing a hat-trick - in fact he scored hat-tricks home and away against Stockport last term - and with the Stockport defence and particularly goalkeeper Conrad Logan starting the match in nervous fashion an early Shrewsbury goal always looked likely.
The visitors managed to survive until the 22nd minute when Cooke rose unmarked to head home a Davies free-kick from six yards.
With the sending-off of Raynes Stockport's mountain became even higher, but they managed to keep Town at bay without being able to seriously threaten the home goal.
When Stockport substitute Paul Tierney took to the field on 68 minutes, he was in direct opposition to brother Marc in the Shrewsbury line-up and on 74 minutes things were all square as Pilkington scored an excellent individual goal, netting with a superb angled drive.
But within three minutes the Shrews were back in front when Davies nodded home six yards to notch his fourth goal of the season.
On 86 minutes Hibbert wrapped up the points, converting from the penalty spot after Town skipper Stewart Drummond had been brought down by Gareth Owen.