Chopra bagged two goals but then left the field claiming the final touch to a Bobby Hassell cross-cum-shot which would have secured him the match ball.
Paul Hart's men, having gone eight games unbeaten, set off in bright fashion and deservedly opened the scoring after nine minutes.
Former Leeds midfielder Stephen McPhail delivered a telling cross from the left and Chopra got in front of Huddersfield keeper Paul Rachubka, to head home from close range.
That lit the blue-touch paper and for the remainder of the half Barnsley were in control.
They extended their lead after 24 minutes when Hassell's low cross from the right appeared to go all the way into the far corner unaided. Yet Chopra was quick to turn away to claim the goal, indicating to his team-mates that he had got the slightest of touches.
Barnsley surged into a three-goal lead seven minutes before the break and it proved to be the best of the lot. Mick Boulding won his aerial battle with Efe Sodje and then slipped the attention of Nathan Clarke before slamming a glorious right-foot shot into the top corner.
The game was turned on its head in the 55th minute when referee Tim Kettle judged that home keeper Ross Turnbull had brought down Luke Beckett.
The referee pointed to the spot and immediately showed Turnbull the red card.
To make matters worse for Barnsley substitute goalkeeper Nick Colgan brilliantly saved Pawel Abbott's initial spot-kick, only for the linesman to order a retake - insisting that Colgan had moved. And on the second occasion, Abbot made no mistake.
Huddersfield made it 3-2 after 70 minutes when veteran striker Andy Booth made no mistake with a header.
The Tykes made the game safe with a controversial penalty of their own three minutes from time after Rachubka appeared to try and elbow Chopra in the box – allowing the on-loan Newcastle forward to seal the points.