While close decisions have dominated the conversation around the technology, the type of blatant mistake that saw Aubameyang flagged offside in the 58th minute is what the system was introduced to eliminate.
United had taken the lead just before half-time through Scott McTominay's first goal at Old Trafford, a fine strike from outside the box, and the game did improve after a distinctly drab start.
But the lack of quality was all too evident and a point for United leaves them 10th with nine points – the first time they have failed to reach double figures after seven games in 30 years – while Arsenal nudged back into the top four.
Paul Pogba and Marcus Rashford were surprise inclusions in the United starting XI having been expected to miss out through injury but Aaron Wan-Bissaka was ill and Axel Tuanzebe started his first Premier League game since May 2017 at left-back.
The 21-year-old's performance was the bright spot of an opening half an hour that showcased everything lacking in both teams.
Driving rain admittedly made conditions difficult but passes were misplaced, crosses over-hit and free-kicks lofted straight out of play.
It took 29 minutes for the first shot and the first really incisive bit of play, with the ball breaking in midfield for Andreas Pereira, who drove at the Arsenal defence and broke into the area before seeing his shot saved by Bernd Leno.
That sparked a bright spell for Arsenal, with Nicolas Pepe shooting over before the Gunners had a good chance to threaten when Pereira picked up a caution for a foul on Matteo Guendouzi only for Granit Xhaka to produce a baffling free-kick that Chambers put behind.
David de Gea made his first save from Pepe at the back post, while Pogba finally found Rashford with a fine through ball only for a combination of a slip from the striker and good tracking from Sokratis to thwart the danger.
Water was bouncing off the sodden turf and a slip from Pereira in the 44th minute let in young Bukayo Saka down the left. His shot across goal was parried by De Gea, who got up well to block the follow-up from Guendouzi.
That became even more important moments later as United broke away down the other end. The chance looked to have gone when James over-hit his cross for Rashford but the striker picked out McTominay 22 yards out and he found the top of the net via the slightest deflection off Sokratis.
After being jeered by his own fans last week, Xhaka's duck of the head as the shot flew towards him will have done nothing to endear the captain to the Gunners faithful.
United wanted a penalty early in the second half for a handball by Sead Kolasinac, but referee Kevin Friend turned down the appeals and it was not deemed enough of a mistake for the decision to be overturned.
However, one replay was all it took to show that assistant Scott Ledger had erroneously raised his flag against Aubameyang after Tuanzebe's awful pass had allowed Saka to play in the striker, who neatly chipped De Gea.
The visitors nearly had a second immediately but the impressive Saka, 18, was denied by a goal-saving block by Victor Lindelof.
United sought a response and Pogba curled a shot just wide before McTominay planted a free header over the bar when he should have scored.
Leno was then called upon to push a strong shot from Maguire over, and the keeper saved his best for last with a diving stop to keep out Rashford's late free-kick.