The Senegal international saw his effort in the 8-0 mauling of Sunderland last weekend taken off him and officially awarded as a Patrick van Aanholt own-goal, but there was no denying the winger seven days later as his strike sealed all three points for Ronald Koeman's side.
Mane, who replaced Shane Long in Southampton's only change following that stunning victory, tucked home the rebound in the first half after Graziano Pelle's shot had bounced back off the upright.
All four previous Premier League meetings between these two sides had ended level, but that trend was bucked as Southampton won for the sixth time in their last seven league games.
It could have been a more emphatic win for the home side, as Morgan Schneiderlin and Pelle struck the woodwork either side of Mane's winner, with Stoke never looking like denying the south-coast club a fourth successive home victory.
The visitors, who came from behind to defeat Swansea City last Sunday, were unable to carve out any clear goalscoring opportunities as Southampton climbed above Manchester City into second, three points behind Chelsea.
Mane went close with a curling effort which flew narrowly wide of the right-hand post in the fourth minute.
Former Southampton man Peter Crouch headed Steven N'Zonzi's cross off target 12 minutes in, before Victor Moses - accused of cheating to win a penalty by Swansea boss Garry Monk last Sunday - beat three men on a mazy run into the area which ended with a tame shot straight at Fraser Forster.
Dusan Tadic tested Asmir Begovic with a low drive in the 29th minute and from the resulting corner, Schneiderlin's strike came back off the crossbar after a well-worked routine involving Tadic and Mane.
Four minutes later, however, the home side took a lead which was no more than they deserved.
After Pelle's initial effort had struck the post, Mane reacted quickest to side-foot the rebound in off the underside of the bar.
Southampton made a strong start to the second period and almost doubled their lead within four minutes as Pelle's header from Tadic's cross bounced back off the bar.
As the game entered the final quarter of an hour, Pelle continued to go in search of his seventh league goal of the campaign, this time heading wide of goal from Tadic's corner.
Mame Biram Diouf, replaced by Jonathan Walters in one of two changes for Stoke, was introduced shortly after half-time by Mark Hughes and almost made a telling contribution 12 minutes from time, just failing to get a proper connection on Phil Bardsley's deep cross from the right.
Hughes threw on Marko Arnautovic and Oussama Assaidi in a bid to force an equaliser, but the visitors were unable to breach a defence which has conceded fewer goals than any other side in the top flight.
