A Peter Crouch headed goal a minute after coming off the bench secured three points for Stoke.
It was a poor game with little creativity or guile; it was more a war of attrition.
The first half was drab, dull and lifeless.
The Potters maybe should have had a penalty when Phil Bardsley looked to have been brought down after Hull failed to clear a corner but nothing was given.
At the other end Sone Aluko skipped past Philip Wollscheid before striking across the face of goal.
Mark Hughes bought Charlie Adam on as a half-time substitute for the injured Stephen Ireland, who Mark Hughes said required between 12 to 15 stitches at the half time break.
The Scotland international nearly had an instant impact when he turned and ran at the Hull defence before shooting narrowly wide.
David Meyler then fouled Adam on the edge of the box. He dusted himself down and fired wide from 20-yards.
Then the turning point, Crouch came on for a frustrated Mame Diouf who had lacked service all afternoon.
Adam played a chipped cross-field ball into the Hull penalty area and Crouch met it to head past Allan McGregor who was rooted to the spot.
The goal from the ex-England international took him level with Alan Shearer for headed goals in the Premier League.
Hull threw caution to the wind bringing on Hernandez and N’Doye but failed to register a single shot on target.
After the match Mark Hughes was left angered by Maynor Figureoa’s tackle on Stephen Ireland.
He said: “Stephen Ireland has been on the end of an horrendous tackle in the first half.
“It’s one that should have seen a red card.
“He’s come in at half-time and rolled his sock down and everyone was taken aback by the severity of the gash. He needed 12 to 15 stitches in the leg wound.”
Hull boss Steve Bruce argued that the Stoke goal was offside: “We’re convinced he (Crouch) is offside and we’ve seen replays which show that.
“I’m not saying we deserved to win the game but we didn’t do enough offensively. Overall I didn’t think we deserved to lose the game.”
Stoke: Begovic, Bardsley, Wollscheid, Wilson, Pieters, Whelan, N’Zonzi, Moses, Walters, Ireland (Adam), Diouf (Crouch).
Hull: McGregor, Elmohamady, Dawson, Bruce, McShane, Livermore, Huddlestone, Meyler (Quinn), Figueroa (Hernandez), Ramirez, Aluko (N’Doye).
Referee: Neil Swarbrick