The final scoreline suggests the Gunners enjoyed a comfortable afternoon against the Potters, but they were made to work hard for a seventh straight success in all competitions.
Rather surprisingly, all three of their goals came from set-pieces - with summer signing Mesut Ozil having a hand in all three.
Wenger was delighted to see his side show a different side to their game, with momentum now firmly behind the north London outfit.
He told Sky Sports: "We had a good first half and the second half was more digging in a little bit.
"We had to dig in because we lost our fluency, you could see that we lacked legs a bit but overall it's, of course, an important three points.
"I didn't expect to score so many headers from free-kicks against Stoke, but the delivery is very important and the deliveries were good today.
"The confidence is there and the desire is there, and that's a very strong
base. We can score goals and create chances, today in the second half we lost
our usual game but in the end we won."
Wenger was forced to tweak his starting XI prior to kick-off when Theo Walcott picked up a knock in the warm-up, with German youngster Serge Gnabry taking his place.
Pressed on what happened to the England winger, who had been struggling through illness in the build-up to the game, Wenger said: "Muscular abdominal problem, but I don't know how serious it is."