Second-half substitute Cameron Jerome was the hero for the home side as he swept the winner home after a great knockdown from Kenwyne Jones with just five minutes left.
That had come after Jonathan Walters had levelled the match following Papiss Cisse's opener just moments into the second half.
The opening 45 minutes was easily forgettable with only a deflected Stoke free-kick which came off Mike Williamson's arm and onto the post, the only effort worthy of note.
But the second half was a different story as just seconds in Newcastle were ahead. Asmir Begovic failed to deal with Demba Ba's 25-yard drive and Cisse latched onto it and fired in off the post.
It was a much-needed goal for the Senegal international, who has struggled to find anything like his form of last season, but it was certainly a preventable one from Stoke's point of view after Glenn Whelan was robbed in midfield.
Newcastle thereafter were happy to counter as Stoke failed to create anything clear-cut. Ba and Cisse both tested Begovic again but he produced two fine saves to keep the visitors from extending their lead.
Begovic's saves proved crucial as Stoke grabbed an equaliser with nine minutes left. Jerome cut inside from the right and crossed for Walters to loop his header into the corner.
From then it was all Stoke as the home side pushed forward and the winner came with just minutes left as Walters' long ball was brilliantly headed down by Jones for an unmarked Jerome to sweep the ball home.
The Britannia Stadium cheered loudly and as the final whistle blew Stoke were able to celebrate climbing into the top 10 while Newcastle remain only two points above the relegation zone.
Stoke boss Tony Pulis will certainly be left feeling pleased with his own decisions after the match as his move to bring Jerome on just after the hour for Charlie Adam proved crucial.