Scannell, who signed a two-year contract extension last month, lashed the ball in from a tight angle on 18 minutes from a pull-back by Nahki Wells.
The move saw Jack Robinson beat fellow full-back Moses Odubajo down the left and crossed for Wells.
His pull-back from the near post ran too far for Grant Holt in the middle but Scannell raced in at the back to drill home.
Holt put Robinson away down the left on 48 minutes and it was his byline cross that led to a second goal for the Terriers.
Scannell threw himself at the ball having steamed in from deep but he was beaten to it by Brentford’s Jake Bidwell – who headed into his own net.
It helped end a five-match winning run for Brentford which had seen boss Mark Warburton named November’s manager of the month.
Derby, Nottingham Forest and Fulham were among the teams Brentford toppled in a surge to third in the table.
They showed how they did it with a slick attacking display that saw them unlucky to be behind at the break.
Alan Judge, who fired wide early on, was denied a goal on 14 minutes when his deflected shot was acrobatically tipped over by Town keeper Alex Smithies.
He also parried a stinging drive which Bidwell struck with the outside of his right boot on 22 minutes.
Brentford created further chances for Alex Pritchard and Championship player of the month Andre Gray but they then fell behind against the run of play.
The home side had claims for a penalty waved away on 32 minutes when Conor Coady was felled by Odubajo.
Bees keeper David Button spilled a 25-yard drive from Jacob Butterfield and Coady went down as he tried for the rebound.
Gray, Brentford’s eight-goal top scorer, fluffed a great chance to equalise in first half stoppage time.
Bidwell put Pritchard in down the left and his defence-splitting pass left Gray in the clear but he scuffed his attempted close-range shot into the turf.
Huddersfield started the second-half like a freight train but though they doubled their lead they never properly killed Brentford off.
Wells, eventually replaced by fit-again striker James Vaughan, missed several good chances, including on 63 minutes when he fired wide from Coady’s pass.
The visitors got a lifeline eight minutes later when Jonathan Douglas tapped in the rebound after substitute Tommy Smith was denied.
Desperate defending ensued as Huddersfield sought to hang on to their first win in five matches.
Smithies tipped over a Judge free-kick on 83 minutes while Town somehow survived a goalmouth scramble soon after.
In stoppage time Brentford substitute Nick Proschwitz missed a good chance with a header from a Bidwell cross.