Substitute Akos Buzsaky came off the bench to land Tony Pulis his first win as Plymouth manager.
The Hungary international midfielder came off the bench to land the winner 12 minutes from time, as Pulis put one over the club that sacked him during the summer.
Buzsaky steered home a left-foot shot after French centre-back Mathias Doumbe set him up by heading back skipper Paul Wotton's free-kick at the far post.
Stoke, however, will be wondering how they did not come away with at least a share of the spoils after totally dominating the first half and twice hitting the frame of the goal.
Paul Gallagher had already rattled the post during the first half before Luke Chadwick rounded French goalkeeper Romain Larrieu to open the scoring for the visitors at the beginning of the second half.
Argyle equalised within two minutes, however, when Northern Ireland international Tony Capaldi's cross was deflected into his own goal by Stoke midfielder Darel Russell.
Hannes Sigurdsson, making his Potters debut as a second-half substitute, then drove the ball against the post from 35 yards before Buzsaky came on and changed the game.
The winner came from the left, from a Wotton free-kick won by David Norris' persistence against Lewis Buxton.
The skipper swung the ball in, looking for a headed touch from Micky Evans at the near post, which appeared to have sent it wide.
However, Doumbe kept the ball alive with a header at the far post, and, when it fell to the young Hungarian, he skipped inside his marker and bulleted in a left-footer low inside goalkeeper Steve Simonsen's near post.
The goal gave Argyle the confidence to see out the remaining time, and they may even have extended the margin when Evans flashed a header wide from the influential Buzsaky's delivery.