The Gunners travelled to the Stade Bollaert-Delelis on the back of a 4-0 thrashing of PSV Eindhoven two weeks ago, while their opponents had made an indifferent start to the Ligue 1 campaign and drew 1-1 with Sevilla in their continental opener.
Arsenal's preparations for matchweek two were disrupted on Monday, though, as inclement weather in London saw their flights delayed and Arteta's pre-match press conference cancelled.
However, the North London giants got off to a strong start in front of an intimidating atmosphere, as Bukayo Saka fed Gabriel Jesus to find the bottom corner following a defensive error from Lens.
Arsenal's joy was short-lived, though, as David Raya's attempted pass to Takehiro Tomiyasu was cut out, and Adrien Thomasson curled home into the top corner with aplomb to draw the hosts level.
Thomasson's strike came not long after Saka was withdrawn due to a muscular injury, and for the most part, Arsenal were starved of opportunities against a well-drilled Lens defence in the second half.
Only a few minutes after Tomiyasu wasted a magnificent chance from a corner - finding himself in acres of space but shooting straight at Lens goalkeeper Brice Samba - Franck Haise's side launched a quick counter-attack, which ended with Elye Wahi notching the winning goal with a crisp first-time strike into the far corner.
Speaking to the media after the game - as quoted by football.london - Arteta refused to blame the flight chaos on Arsenal's lacklustre display and congratulated Lens on a stellar defensive display, saying: "No, let's not put excuses.
"First of all, congratulations to Lens. They are a really good side. Really well coached. We knew it was going to be a really tough match. I think we started the game and got a grip of the game, straight away they scored a goal.
"We were in total control at that moment. From just one isolated situation we conceded from and it was game on, we started to second half really well again. Had a huge chance with Leo to make it 2-1. Not only that, we were preparing subs as well. Tomiyasu has a big chance and when they go the other way, they score.
"The difference between today and PSV is clear. In the boxes, we had four or five chances we didn't put away and we didn't defend the boxes well enough.
"It's true there were moments in the second half we struggled to be more threatening in the final third and find spaces. They defended with those numbers really good. That's something to take for the next game."
With PSV and Sevilla playing out a 2-2 draw in the other Group B game on Tuesday, Arsenal remain in the top two spots despite their disappointing night, albeit now one point below new group leaders Lens.
Arteta also delivered an update on Saka's injury following the Englishman's first-half substitution, as the Gunners wait to learn the extent of his muscular issue ahead of Sunday's crunch Premier League clash with Manchester City.
Following the October international break, Arsenal return to Champions League action away to Europa League holders Sevilla on October 24.