The Terriers had seemed to be on course for a hard-fought point until Lucas Torreira struck the winner seven minutes from time.
It was a goal worthy of winning an absorbing contest as Torreira’s overhead kick broke Town’s resistance after tremendous work from Pierre-Emerick Aubameyang.
But David Wagner’s side could still feel hard done by on an afternoon when Alex Pritchard and Laurent Depoitre had penalty appeals turned down by referee Paul Tierney.
The official had also left the home fans irate just before the break in what up until Torreira’s late winner had been the game’s big talking point.
An underhit back pass by Mathias ‘Zanka’ Jorgensen set Alexandra Lacazette free and he duly beat Jonas Lossl.
His celebrations, however, were quickly cut shot by a linesman’s flag raised due to the Gunners striker being offside moments before Jorgensen’s error when trying to latch on toa flick by Pierre-Emerick Aubameyang.
Lacazette was fuming, his anger no doubt fumed further by his own glaring miss shortly before the half-hour mark.
Set up by Matteo Guendouzi, the Gunner striker slipped at the vital moment and his shot cleared the crossbar by some distance.
Aubameyang had been equally culpable a few moments earlier when he shot wide after Town had been opened up by some slick passing.
Huddersfield’s best best moment in the first half came when Tommy Smith found Alex Pritchard but he fired over.
Pritchard turned creator in the second half but his drilled cross intended for Laurent Depoitre was cut out by Bernd Leno in the home goal.
Arsenal continued to carry a threat and Aubameyang headed wastefully wide from a Granit Xhaka corner before Sead Kolasinac failed to capitalise when played clear behind the visitors defence.
At that stage, Town looked on course for a precious point but Torreira had other ideas.
Huddersfield manager David Wagner said: "Obviously it is hard to take but I can see the positives. This was a proper fight which the players gave Arsenal. We did so many things right and limited their qualities. Unfortunately the result is what it is.
"We frustrated Arsenal, how the players did it tactically, and the shift they put in, was brilliant. Our tactics worked but unfortunately this goal was an unlucky one because the rebound and second rebound went to Arsenal."