Goals from Ricardo Fuller and Liam Lawrence saw the Potters move up to 12th in the Premier League table with only their second away win of the season.
Hull came close early on as Craig Fagan won the ball on the right flank and curled in a left-footed cross towards the head of Daniel Cousin, whose neat effort from eight yards had to be cleverly tipped over the bar by keeper Thomas Sorensen.
Richard Garcia then came close for the home side as Nick Barmby found the Australia international with space inside the box, but the midfielder's low right-footed shot was well saved by Sorensen.
Lawrence tried his luck for Stoke midway through the half as he attempted a speculative half-volley from the right side of the box, but the midfielder saw his shot dip just over the crossbar.
Stoke then came within inches of taking the lead as a deflected shot from Lawrence whistled just past the post.
The visitors did take the lead from the following corner as Hull failed to clear a Matthew Etherington out-swinger, allowing frontman Fuller to turn and slam the ball home from eight yards.
Hull came close within seconds of the second half as Kevin Kilbane picked up a loose ball in the box and curled in a left footed effort, but Sorensen managed to turn the ball round the post for a corner despite seeing the ball late.
Glenn Whelan then fired in an ambitious effort that nearly paid off for the visitors as the Irishman struck a half-volley from 35 yards which dipped just over the crossbar.
Sorensen was called into action again moments later as Barmby delivered a pinpoint cross from the left onto the head of Garcia, whose effort from 10 yards had to be well saved by the Danish keeper.
Whelan then came even closer to doubling Stoke's lead as the midfielder picked up the ball on the edge of the box and hit a looping volley which came back off the right upright.
Tony Pulis' men did double their lead on 73 minutes when Lawrence picked the ball up on the right and fired in a spectacular effort from 25 yards which flew past the hapless Boaz Myhill and into the corner of the net.
Andy Dawson pulled one back for Hull in injury time with a curling left-footed free-kick, but it proved to be too little too late for the Tigers.