Dimitar Berbatov and John O’Shea scored the goals for United at the Britannia Stadium.
“The best team won today,” said the Stoke chief. “They controlled the ball well.
“We have to be at our best, everybody having a go and everybody playing at their top, to be able to compete against a top-four team.
“We did that a couple of weeks ago against Chelsea and gave them a real run for their money.
“But we were a little bit flat today. There were four or five who just weren’t really on top form.
“When you play the better teams in the league, then everyone has got to be on their top game and they have got to be off it.
“We know where we are at the moment, and where we are trying to get.
“Credit to Manchester United. They are the champions and everybody knows the quality they have got.
“We will take it on the chin, pick ourselves up and get going again on Monday.”