Jon Walters converted from the spot on the 76th minute to deliver a hammer blow to the Gunners' title aspirations, but Wenger felt there was nothing his defender could do to get out of the way of the ball.
"It was a nice gift from the referee," he told reporters. "Koscielny is one yard away. He has no time. How can he take his hand away? He has no chance."
The Frenchman also admitted that the defeat was a huge blow in his side's pursuit of the Premier League title, with the north Londoners now three points off the top after Chelsea's victory at Fulham.
"It is a big worry not to win a game like that," he said. "It's a massive setback.
"We didn't produce the performance that we wanted. To win a title, you have to perform when you're expected to.
"It was a good defensive performance and overall I think we were unlucky to lose this game. Offensively we didn't create enough. Our offensive game was poor considering our standards. At the end of day we didn't score.
"I don't assess our title chances at all. We just have to play well in the next game."
Stoke boss Mark Hughes disagreed with the Arsenal boss over the penalty, insisting that it was the correct decision from Jones.
"I know Arsenal don't think it was a penalty but I'm a bit bemused by that," he said. "I think it was clear-cut to most people.
"They can't have any real complaints. We showed more intensity and drive and determination. They struggled against that."
Hughes was also quick to praise Walters' charcater in stepping forward despite his checkered recent history from the penalty spot.
"That's what you'll get from Jon because he's mentally very strong" he said. '"He's a senior player in the group and he takes responsibility each and every day.
"It doesn't surprise me that he grabs the ball, he wasn't going to give it to anyone else and I was really pleased for him that he was able to dispatch it because it was a pressure penalty, obviously."
"The stars were aligned and it came together," Hughes added. "I thought we were excellent on the day to be honest, going up against a very accomplished Arsenal side with a lot of talent and a lot of ability, but I thought we matched that and in the end we've won the game courtesy of a penalty.