Pilkington, who recently signed a new two-year deal, curled in an exquisite shot from 25 yards midway through the first half - the only goal of the game at the Galpharm Stadium which was televised by Sky Sports.
The visitors, who had not played since losing 5-1 to Exeter 16 days ago, were denied an equally-spectacular leveller when Clinton Morrison's stunning volley after 50 minutes was ruled out for offside.
The game started like lightning, with Town's Jordan Rhodes being foiled by a great save from Owls goalkeeper Nicky Weaver straight from the kick-off. The Terriers were then denied what looked a certain penalty when Morrison handled from the resulting corner.
Huddersfield goalkeeper Alex Smithies made a brilliant double save to keep out Darren Purse and Jermaine Johnson after 31 minutes as Wednesday hit back. Weaver was then at it again with a stunning stop to keep out Scott Arfield's piledriver late in the first half.
The second 45 was marred by several bad-tempered confrontations but Huddersfield clung on to register a first league win in four outings and their first double of the season following a 2-0 win at Hillsborough in November.