Pawel Abbott's instinctive first half bicycle kick kept Huddersfield on course for automatic promotion, but Town struggled for long periods against mid-table Southend.
Striker Abbott turned to net on 13 minutes after Andy Booth had flicked on Tony Carss' long throw from the right.
Tyne and Wear based referee Eddie Ilderton played advantage, despite Booth taking a heavy thump in the back from Shrimpers defender Mark Warren, and the goal was allowed to stand.
It was Pawel Abbott's fifth goal since signing from Preston in February and he will be missed when he starts a three-match ban next Saturday for his sending off at Leyton Orient last week.
But the effort was enough to end the Shrimpers' eight game unbeaten run - although it did not reflect the visitors having most of the ball during the match.
Southend controlled most of the play in the first half without really testing the Town defence but after the break they should have secured a deserved equaliser.
Mark Bentley hit the underside of the crossbar with a great free-kick on 63minutes awarded for David Mirfin's trip on Drewe Broughton just outside the box.
Minutes earlier Mirfin had been booked for a high tackle on Carl Pettefer- who was taken off injured in agony.
But the enforced sub, in which Tes Bramble replaced the injured Pettefer, did not effect Southend's momentum as they piled on the pressure in search of a leveller.
And it was Bramble who nearly secured Southend a deserved point with an overhead kick following a goalmouth scramble on 72 minutes.
Panic was caused among Huddersfield's defenders by Mark Gower's byeline cross that nobody seemed willing or able to clear.
Broughton pounced on the loose ball and set up Bramble but his overhead kick flew inches over the bar.
Referee Ilderton added four minutes of stoppage time as a result of Pettefer's injury and it seemed to last for hours for the home side's nervous fans.
Southend searched in vain for an equaliser, when the final whistle was blown there was much relief around the McAlpine Stadium.
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