First half goals from Alex Iwobi and Alexandre Lacazette ensured a victory that retains Emery’s interest in a top-four finish just days ahead of a visit to Belarus to face BATE Borisov in their Europa League last 32 first leg tie.
But Arsenal are still without a clean sheet on their Premier League travels this season after conceding an injury-time consolation to their struggling hosts.
Indeed, Emery cut a frustrated figure in the Arsenal for long spells of the first half, the Spaniard becoming increasingly animated as his side failed to punish the division’s poorest team adequately.
Still, two goals was just about the correct half-time scoreline on the balance of play, even if the second of those only came in the closing minute of the opening period.
It was a goal that summed up the defensive problems that have blighted Huddersfield all season long, three defenders crowding out the breaking Henrikh Mkhitaryan but failing to dispossess him.
He slipped the ball wide to full-back Ainsley Maitland-Niles and his low cross picked out the unmarked Lacazette who rammed the ball into an open net.
The opening goal had also exposed Huddersfield’s chronic defensive frailties, although there was a large dose of good luck to go with the poor goalkeeping of Ben Hamer on 15 minutes.
After a quick free-kick, Mkhitaryan freed Sead Kolasinac down Arsenal’s right and his hanging cross was met by Iwobi.
His acrobatic, first-time volley took a deflection off Terence Kongolo but should still have been kept out by Hamer who flapped at it with one-hand and succeeded only in helping it into the goal.
In between the two Arsenal goals there were, at least, spells of Huddersfield pressure, which went some way to explaining Emery’s anger on the touchline.
Terence Kongolo shot directly at Bernd Leno on Huddersfield’s first meaningful foray into the Arsenal area and, on 25 minutes, the Gunners could consider themselves fortunate to survive a strong penalty appeal from the home side.
A powerful shot from Jason Puncheon struck Laurent Koscielny, who clearly handled as the ball struck him although unintentionally, according to referee Jonathan Moss.
If Emery had cut an unhappy figure at times in the first half, he was positively apoplectic in the first five minutes of the second as his side appeared hell bent on gifting Huddersfield a way back into the contest.
First, Maitland-Niles inexplicably gifted the ball to Adama Diakhaby, 25 yards from goal, whose first-time shot was dealt with, comfortably enough, by Leno.
And then Arsenal’s defence was badly stretched as Kongolo exchanged passes with Aaron Mooy and crossed for Diakhaby whose crisp, first-time shot was well saved by the Arsenal keeper.
There was also an enterprising run and deflected cross, which just cleared the visitors’ goal, and a Puncheon drive that Diakhaby failed to turn in at the far post.
But the home pressure simply left Huddersfield more susceptible to the counter-attack. Arsenal substitute Mohamed Elneny headed over from six yards, from a Kolasinac cross and Iwobi should have wrapped up the points, from a Mkhitaryan through ball, on 70 minutes but succeeded only in shooting directly at Hamer.
The home side finished strongly with Laurent Depoitre flashing a shot inches side and Nacho Monreal being required to clear off the line from Karlan Grant.
And deep in injury-time, Diakhaby broke clear on goal, lifted the ball over Leno and watched as Kolasinac turned into his own goal via an unfortunate deflection.
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