Pierre-Emerick Aubameyang's 38th-minute strike earned the Londoners their first away points of 2018, but their sixth-place league finish is the worst of Wenger's reign.
The pressure was off Huddersfield after Wednesday's 1-1 draw with Chelsea secured their top-flight status, and the Terriers took that momentum into the opening 15 minutes as they created three chances.
Steve Mounie was an aerial threat for Huddersfield all day, firing Arsenal a warning shot when he met Alex Pritchard's third-minute cross with a well-directed effort that was theatrically pushed away by David Ospina.
Another towering header from Christopher Schindler two minutes later was nervously cleared off the line by Rob Holding, but the hosts were not limited to a set-piece threat as they twice cut Arsenal apart in open play.
Pritchard spotted the run of Tom Ince into the box, only for the winger to blaze over the crossbar from 12 yards, and the same combination endangered Arsenal's goal with a left-footed drive that flashed just wide.
It took until the 28th minute for Arsenal to forge a chance themselves as Sead Kolasinac knocked the ball wide after a corner had somehow reached him at the back post. Henrikh Mkhitaryan followed suit moments later when his deflected half-volley from the edge of the box went the wrong side of the post.
It was not a vintage Wenger performance, but Arsenal put together one move of real class as Mkhitaryan and Alexandre Lacazette combined to release Aaron Ramsey for a cross which Aubameyang stretched to convert from six yards - his 10th league goal in 13 matches since joining from Borussia Dortmund.
The second period began in similar fashion to the first, as a clever reverse pass from Pritchard set up Ince for a low drive across goal which stand-in stopper Ospina pushed around the post.
Huddersfield continued to push for an equaliser but Arsenal defended with robustness that they have rarely displayed in a season in which they have conceded a club-record 51 goals in the Premier League era.
Having said that, the Gunners had to ride their luck late on, after both Lacazette and Danny Welbeck had spurned opportunities to seal all three points by shooting straight at Jonas Lossl when one-on-one.
Midfielder Aaron Mooy has been Huddersfield's standout performer across the campaign and it would have been apt had his 89th-minute volley that thundered back off the crossbar earned the hosts a deserved point.
Laurent Depoitre also came close with the last action of the game as Ospina just about kept his header from crossing the line at the second attempt, also blocking the follow-up attempt from Mathias Jorgensen.
The Terriers finish 16th in their first attempt at the Premier League and will be back again next year, although they will be facing a very different Arsenal as the post-Wenger era begins in North London.
HUDDERSFIELD (4-2-3-1): Lossl; Hadergjonaj, Zanka, Schindler, Kongolo; Mooy, Hogg (Whitehead, 87'); Lowe, Pritchard, Ince (Depoitre, 61'); Mounie (Billing, 79')
ARSENAL (4-2-3-1): Ospina; Bellerin, Mustafi, Holding, Kolasinac (Monreal, 68'); Xhaka, Ramsey; Iwobi (Maitland-Niles, 72'), Mkhitaryan; Aubameyang (Welbeck, 67'); Lacazette