Both sides struggled to find any kind of creative outlet in the opening 15 minutes as they passed without a notable incident.
Ian Westlake should have done better when Darren Bent played the ball into his path on the left of the area but Ed de Goey stood strong and saved with an outstretched leg.
It took 36 minutes for the home side to take the lead when Sebastian Svard was brought down by Georges Santos to concede the penalty.
Peter Hoekstra stepped up to the spot and confidently struck the ball home into Kelvin Davis' bottom-right corner leaving him no chance.
Ipswich attempted to shake up the game with the addition of Richard Naylor and Driss Diallo but it remained much the same with Stoke having the better of the play.
The Potters went further ahead in the 68th minute despite calls for offside when Gifton Noel-Williams flicked the ball on to play Ade Akinbiyi clean through and he neatly rounded the oncoming Davis before tapping home from six yards.
A late flurry from the Tractor Boys battered the City goal but a fine save from de Goey and solid defending was enough to claim the points.