Wenger, who announced he would be leaving the Emirates at the end of the season just over three weeks ago, was given a fitting send-off at the John Smith’s Stadium.
Aubameyang struck seven minutes before the break to ensure the 68-year-old Frenchman signed off his 22-year reign with a win in his 1,235th and final game in charge.
Huddersfield boss David Wagner made a special presentation in the tunnel before kick-off and Wenger was given a guard of honour by both sets of players.
Huddersfield, celebrating their unlikely Premier League survival after Wednesday’s draw at Chelsea, did their best to help mark the occasion.
But as the home fans revelled in a party atmosphere it was soon apparent Wenger’s players would have to fight hard to clinch a win for their boss.
Town striker Steve Mounie went close to giving his side an early lead when his downward header was well saved by David Ospina and then Tom Ince blazed over from in front of goal following Alex Pritchard’s cross.
A sell-out crowd gave Wenger a standing ovation in the 22nd minute in tribute to his 22-year Arsenal career and his side finally began to warm to their task after a slow start.
Sead Kolasinac failed to get enough on Henrikh Mkhitaryan’s corner at the far post but the Londoners were rewarded for a dominant spell towards the end of the first half when they took a 38th-minute lead.
Alexandre Lacazette’s pass set Aaron Ramsey free down the left and the Arsenal captain’s precision cross to the far post was turned home by Aubameyang.
It was the former Borussia Dortmund forward’s 10th goal for Arsenal since arriving in January.
Huddersfield took the game to Arsenal in the second period without seriously testing Ospina until the 60th minute.
Ince raced onto Pritchard’s pass and his low shot arrowed towards the bottom corner, only for Ospina to divert it for a corner with a fine save.
It was Ince’s final act as he made way for striker Laurent Depoitre.
Wenger replaced Aubameyang and Kolasinac with Danny Welbeck and Nacho Monreal with 24 minutes left but it was Town who continued to carry the greater threat.
Ainsley Maitland-Niles stepped off the Arsenal bench for Alex Iwobi before the Gunners misfired with two clear-cut chances which would have settled the match.
Lacazette fired straight at Huddersfield goalkeeper Jonas Lossl when through one-on-one and Welbeck was also thwarted by the Denmark international in similar circumstances soon after.
Town midfielder Dean Whitehead, set to retire and join the club’s coaching staff, was given a rousing reception when he replaced Jonathan Hogg in the closing stages.
The home side went close to spoiling it for Wenger in the dying embers when Aaron Mooy’s thumping volley skimmed the crossbar and Depoitre’s header was snaffled by Ospina.