In the week when the Gills were forced to sell talismanic striker Marlon King to ease their financial problems, they always had the edge over Stoke, who have now failed to win any of the last seven league meetings between the two sides.
Apart from Pulis, there was also a return to a former club for his assistant Lindsay Parsons and two players, Carl Asaba and Ade Akinbiyi, both Gills top scorers in the past.
It proved a frustrating afternoon for Asaba, booed everytime he touched the ball, and who had to be warned by referee Grant Hegley after exchanging words with assistant referee Mark Russell.
Asaba's high point came when he set up Stoke's consolation effort for John Eustace to convert, and set up an interesting finish.
Gills keeper Jason Brown also denied Stoke the prospect of a second-half comeback with excellent saves to keep out efforts from Kris Commons and Akinbiyi.
Gillingham, unchanged from the team that drew at Coventry the previous week, went in front when Paul Shaw fired scored just before the half hour.
It was Shaw's sixth of the season, putting him top of the Gills scoring list, one ahead of King, while Chris Hope headed in his second of the season to convert Nicky Southall's corner in the dying seconds of the first half.
Frazer Richardson then struck a home post with a wind-assisted effort, only to see play halted for an infringement inside the box against his side, and both teams used all three substitutes before Gillingham grabbed the points eight minutes from time.
It was Kevin James, who had earlier replaced Tommy Johnson, who made the most of a mistake on the edge of his box by Stoke keeper Ed de Goey. The ball found it's way to Mamady Sidibe and he made sure of the points with his third goal of the campaign, which went in after striking a post.