Danny Higginbotham opened the scoring on two minutes and Darel Russell wrapped up the win in the 80th minute with a low shot from 18 yards.
The Potters took the lead almost immediately as a lack of concentration in the Hull defence allowed an unmarked Higginbotham to head in Lee Hendrie's corner from six yards out.
Stoke came close to adding a second goal soon after as a quick Hendrie free-kick found Liam Lawrence in space but his header from six yards was neatly palmed to safety by Boaz Myhill.
Jason Jarrett tried his luck from distance moments later but his 30-yard shot was well saved by Steve Simonsen in the Stoke goal.
Dean Marney was next to try his luck from distance for Hull but his 25-yard pile-driver was again saved by the on-form former Everton and Tranmere man Simonsen.
Craig Fagan then found himself with space inside the box after a long throw from Stuart Elliott, but he couldn't keep his ten-yard shot down as it flew over the bar.
Hull almost equalised early in the second half as Marney won a free-kick on the right-hand side of the Stoke box. Elliott struck it left footed and the ball looked to be heading towards the top corner but Simonsen did well to turn it over the bar.
Elliott tried to level again midway through the half but his left-footed volley from the edge of the box was once again saved by the outstanding Simonsen.
Stoke sealed the win with 10 minutes to go as Russell collected the ball just inside the box and slid the ball left footed past Myhill.