Arsenal's title hopes suffered a major setback at the Britannia Stadium courtesy of Jonathan Walters' spot kick 14 minutes from the time.
The penalty was awarded after Laurent Koscielny handled Walters' flick-on inside the box and the Irishman's calmness under pressure from the spot ensured Arsenal were sent home without a win for the ninth time in 10 trips to Stoke.
But visiting manager Wenger insisted that his side had been hard done by.
"We conceded a goal that was a nice gift from the referee but it can happen," Wenger said of official Mike Jones' decision.
"He's (Koscielny) one yard away, how can he take his hand away? He has no time to take his hand away from the ball. He has no intention at all."
Wenger did concede, however, that Arsenal, who slipped four points behind leaders Chelsea, were below par in the final third.
"We had a good defensive game and we were unlucky to lose the goal, but offensively we didn't create enough," the Frenchman added.
"I feel going forward we were not good enough to create chances and that's why we got punished.
"You have to give credit to Stoke, they defended well, with resilience, they made the game very physical. We knew that before the game, they have the highest number of fouls in the Premier League. We didn't cope well enough with it."
