They made the perfect start when Rory Delap gave them a fourth minute lead but ultimately had to secure their success the hard way after goals from Rob Edwards and Andy Keogh two minutes either side of half-time put Wolves in control.
But a 49th minute goal from the impressive Liam Lawrence drew Stoke level before Leon Cort and Fuller powered Stoke to only their second win at Molineux in 25 games.
The defeat continued a woeful run of form for Wolves that has seen them slide out of the promotion race on the back of a haul of just ten points from the last 36.
Rob Edwards gifted Delap his early opener when his under-hit back pass failed to reach Wayne Hennessey.
Mamady Sidibe beat Hennessey to the ball and crossed for Delap to head into an empty net from six yards.
Stoke should have doubled their advantage 11 minutes later but an unmarked Cort somehow missed the target with a close-range header from Lawrence's corner.
That let-off finally sparked Wolves into life only for McCarthy's side to squander two gilt-edged chances in the space of three minutes.
Sylvan Ebanks-Blake volleyed over the bar after good work by Keogh in the 22nd minute.
Kevin Kyle then missed an open goal from three yards when he just failed to get enough contact on the ball after Steve Simonsen was unable to hold a powerful low drive from Dave Edwards.
Wolves' pressure finally told on the stroke of half-time thanks to another right-wing cross from Keogh.
Kyle forced the ball back across the face of goal and Rob Edwards was on hand to make up for his earlier error when he stabbed his shot past Simonsen for his first goal since joining Wolves from Aston Villa three-and-a-half years ago.
Wolves started the second half as they had ended the first and took charge when Kyle volleyed a Kevin Foley free-kick into the path of Keogh who rifled home his seventh goal of the season with a low angled drive.
But Wolves' joy was short-lived as Glenn Whelan released Lawrence who surged into the area before beating Hennessey with a rising drive for his ninth goal of the campaign.
Cort then set the seal on the Stoke fightback after Wolves failed to deal with a Lawrence corner.
Sidibe saw his header tipped on to the bar by Hennessey but Cort reacted fastest to the loose ball and stabbed home at the far post.
To rub salt into the Wolves wounds they had last minute claims for a penalty rejected when Rob Edwards went down under a challenge from Salif Diao.
Stoke surged straight up the field and Fuller struck with a low angled drive.