The Potters boss expressed his belief that the 31-year-old deserved to make the England squad, but backed him to overcome that disappointment by performing well next season
The striker impressed for the Potters last season, scoring 14 goals, including a stunning volley against eventual champions Manchester City in March.
And Pulis believes Crouch can use the disappointment of failing to make Roy Hodgson's squad as a platform to perform well again next season.
"I have spoken to Peter and he was very disappointed to be left out - and rightly so," Pulis told The Sentinel.
"I just said to him to go away and have a good family break, then come back raring to go for next season.
"I've no real worries with Peter because he's an experienced lad and knows the score. If anything, his omission will be more of a motivation and he'll come back flying."
The Welshman also insisted Crouch's performances last season merited an inclusion ahead of Andy Carroll, Wayne Rooney, Jermain Defoe and Danny Welbeck.
"I'm desperately disappointed for him. First and foremost I think he deserved to be picked," added Pulis.
"His performance levels have been absolutely outstanding for us and no disrespect to one or two who have been selected, but I think he's in front of them.
"But it's up to Roy Hodgson to pick his team and good luck to them."
Stoke chairman Peter Coates echoed his manager's views and suggested that Crouch would have been selected if he was playing for a bigger club.
"I think it is self-evident that your chances are enhanced if you play for one of the perceived glamour clubs," he said.
"I am disappointed for Peter. He's had a great season and, in my opinion, deserves to be in the squad. He's a wonderful player who has been a tremendous asset to the team."