The boss was again forced to juggle his back line with Laurent Koscielny, Nacho Monreal and number one goalkeeper Wojciech Szczesny all missing through injury.
It meant Wenger handed rookie stopper Damian Martinez only his fourth Premier League appearance of the season, while Calum Chambers filled in at centre-back with 19-year-old right-back Hector Bellerin also starting.
And the makeshift defence was torn apart in the opening half, Peter Crouch giving the Potters the lead after only 19 seconds, with former Barcelona forward Bojan and Jonathan Walters also scoring to open up a 3-0 half-time lead.
Arsenal improved after the break and the comeback looked to be on with two quick-fire goals from Santi Cazorla and Aaron Ramsey, but the resurgence came too late to claim a share of the points.
Chambers' late sending-off for a second yellow card only added to the visitors’ task, and Mark Hughes' side eventually held on to secure a deserved three points.
“Stoke started very strong, you have to give them credit for that, and we were not decisive enough defensively,” said Wenger.
“We gave them a really good present [for the first goal] and from then on it was difficult for us.
“We put a lot of energy into the game and in the second half we had good opportunities to come back, but unfortunately we couldn’t do that
“We were too tender at the back from the start and when we eventually began to respond it was too late.
“We were a bit too inexperienced in defence because we couldn’t play Koscielny or Monreal and with Wojciech being out as well we were maybe a bit too soft to cope against them.
“I feel we were a bit unlucky because the third goal was a foul on the corner, but still we were not good enough defensively today.”
The Frenchman also defended his decision to start Danny Welbeck on the bench, with the England forward – who has scored 11 goals for club and country this season – making a telling contribution when he replaced the under-siege Bellerin at half-time.
He added: “Danny has played a lot and he could have played today from the start, but he had a little groin problem and I rotated a little bit because I wanted to give him a breather.
“I had to respond at half-time, unfortunately, but he looked ok.
“We have three or four strikers here and [Alexis] Sanchez has played every game, he has to dig deep now in every game, so at some stage you have to rest the players.”

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