Yaya Toure scored a second-half goal as City emerged victorious in a one-sided final in which captain Carlos Tevez and his team-mates outclassed their opponents.
Pulis said: "We've reached a level of performances over the last six or seven weeks, beaten Newcastle and Wolves and Arsenal and come to Wembley and beaten Bolton very convincingly. "The greatest disappointment is that we have not reached that level."
He added: "They are disappointed with themselves for not reaching that level. Manchester City were the better team. They deserved to win the game. You need to bring your 'A' game to the table.
"We have had a great season. To be eighth in the Premier League, to have got to an FA Cup final, to stay in the Premier League for a fourth consecutive year and to be in Europe next season is a fantastic achievement."
Pulis, who saw goalkeeper Thomas Sorensen make two flying saves from Carlos Tevez and Balotelli, put Stoke's disappointing showing down to having lost key players such as Ricardo Fuller and Danny Higginbotham.
He said: "Maybe we ran out of a few players. Ran out of a bit of depth that Manchester City have got. They're human beings, but they've been fantastic and they are desperately disappointed."
The Stoke boss also saluted City`s supporters who stayed to watch the cup being presented and whose enthusiasm made the occasion as vibrant as Wembley has seen in years.
He said: "Our supporters were fantastic. To be there at the end of the game to watch another side pick up the trophy is pretty unique.
"The club has been a community club. It's the closest I've ever known a group of supporters to get with a football club. It's been pretty phenomenal."
Source: PA
Source: PA