Stone, now recovered from a hamstring injury, ran through a hastily re-organised Wolves defence to beat Matthew Murray with a shot which the keeper blocked but could not prevent from entering the net.
Murray was not called on again to make a serious save and nor was home keeper Shaka Hislop.
Wolves' leading scorer Kenny Miller and Portsmouth's Svetoslav Todorov, with 37 goals between them, were both substituted after disappointing performances which mirrored the difficulties both sides had in creating chances.
For Champions-elect Portsmouth it was their 23rd win in 37 matches but for Wolves the defeat cast new doubts over their play-off prospects.
Wolves manager Dave Jones faced pre-match problems when three of his back four defensive unit were ruled out by injuries and illness.
Joleon Lescott picked up a thigh strain in training, Lee Naylor contracted a virus and Paul Butler was unable to play because of concussion.
Paul Ince was restored to the Wolves midfield after suspension but was booked again for a foul as the battle for points intensified.
Wolves sent on Adam Proudlock in place of Miller while Colin Cameron failed to re-appear for the second half but Portsmouth did enough to clinch a victory.
Nigerian striker Yakubu Ayegbeni blasted a shot straight at Murray as Wolves pressed forward in search of an equaliser but neither side produced anything like their best form.
Stone marred a useful return to action by getting himself booked in the 86th minute for a foul on Ince and there were also cautions for Alex Rae and Cameron of Wolves and Portsmouth's powerful Australian defender Hayden Foxe.