The winger fell over in his own penalty area following an innocuous looking challenge but sustained what looked to be a badly broken leg.
The game was delayed while Pilkington received treatment before being rushed straight to hospital as nine minutes of stoppage time were added on.
Earlier, Town's Benik Afobe finished neatly from close range when a Jordan Rhodes shot bounced off a Rochdale defender and into his path.
Huddersfield's Gary Roberts produced an exquisite chip out of nothing to make it 2-0 in the 33rd minute. He was surrounded by three Rochdale players on the edge of the box but managed to find the net from a seemingly impossible position.
Rochdale, though, nearly grabbed a point as Will Atkinson hit the post and Town goalkeeper Alex Smithies produced a brilliant save to tip over a bullet header from Jean-Louis Akpa Akpro in the ninth minute of stoppage time.