Arsenal got off to a slow start at the Bet365 Stadium with Stoke looking livelier from the off. Fletcher broke down the middle and found new signing Jese Rodriguez, the Spaniard skipping past Mustafi and to get his first shot on goal which was blocked by Petr Cech.
The Gunners gradually began to claim control, pushing the hosts back. However, chances continued to be scarce with Stoke's back line remaining strong.
Wenger's team found a way through down the left-hand channel, where Zouma and Diouf struggled to cope with attacks. Ramsey and Welbeck found space inside the area forcing Butland into action.
Arsenal's dominance continued throughout the half, Ramsey side-footing the ball at Butland and Xhaka having a go from distance, but there was no breakthrough before half time.
And it was Stoke who surprisingly took the lead after the break. Jese Rodriguez started the move finding Berahino out wide, the Spaniard continued his run and got the return ball inside the box before drilling a low shot across Cech and into the bottom corner.
With the stadium buzzing with the unexpected opener, Arsenal looked stunned. The visitors were initially taken aback, but endeavoured to find an appropriate response. Chances came their way, but Butland's fantastic display continued.
The keeper did spill Bellerin's shot and Welbeck almost managed to latch onto the ball before, moments later, the striker hit the roof of the net. Ozil's cross awarded him plenty of time and space to pick his spot with a header, but it came off his shoulder and drifted over the bar.
Mustafi crossed for Ramsey to toe-poke his effort towards goal, before Stoke were at the other end, Cech palming Berahino's bouncing header over the bar.
Wenger introduced substitutions to the match, among whom was striker Olivier Giroud, and Mark Hughes decided to rest goalscorer Jese Rodriguez, who received a standing ovation from the home crowd.
Lacazette fired a powerful shot high into the net and Arsenal thought they had an equaliser, but he was called offside in what turned out to be a very tight call.
Giroud had one last chance, glancing a header wide after Monreal drilled a cross towards the Frenchman, but Stoke managed to hold on for all three points thanks to Jese Rodriguez's goal.