Newcastle took the lead through Christian Atsu, who was the quickest to meet Matt Richie’s cross from the right-hand side.
However Stoke hit back through Xherdan Shaqiri, firing home from 20 yards to level the score.
It was the captain once again though to send Newcastle home with three points, as Jamaal Lascelles rose highest to meet a corner and powered home.
Toon-tastic first half
Both sides started strongly, as the rain poured down on St. James’ Park in the early exchanges.
Rafa Benitez came into this game after a win against Swansea City last week, and is unbeaten against Stoke in all five Premier League fixtures he has played against them. Winning two and conceding just the single goal.
His Newcastle side began to pick up steam early on, as DeAndre Yedlin’s low cross was well intercepted by budding England number one Jack Butland.
Newcastle’s possession then began to count, as Atsu put the Toon ahead after 19 minutes.
Atsu was able to turn home a brilliant cross by Richie, who has been in spectacular form recently for Newcastle.
The goal was Atsu’s first ever in the Premier League, and came at a great time as Newcastle then went from strength to strength.
Captain Lascelles almost scored his second goal in two games as he was able to meet a corner well but his free header flew just wide of the post.
Stoke then hit back through Shaqiri, who bent a speculative effort that was making its way to the top corner before Rob Elliot managed to tip the shot over the bar.
Newcastle came close to getting a second, after Butland made a fine save to deny Joselu a goal against the side that sold him this summer.
Joselu was a mere five yards away from goal, but was unable to poke the ball past Butland following Yedlin’s deflected shot.
Second half more of a contest
Newcastle usually start the second half slowly. In the 46-60 minute duration of play in their games this season, Newcastle have conceded 10 shots, more than in any other 15min period.
What has been more worrying is the quality of shot they are conceding in this timeframe, allowing 0.23 xG/Shot, way higher than any other 15 min period. Numbers via Understat.
However they started strongly, just seconds after the restart Joselu found himself in an acre of space inside the area but skied his shot as he tried to make Stoke rue selling him.
It was that time period that cost Newcastle once again though, as Shaqiri tied the score up in the 57th minute.
The Swiss international drifted inside onto his favoured left foot and bent an effort into the bottom corner from 20 yards.
Shaqiri then had another effort just minutes later from a similar area, but this time his shot flew way over the bar.
Shaqiri has now scored eight Premier League games for Stoke, with six of them coming from outside the penalty area.
Mame Biram Diouf forced a magnificent save from Elliot as the wing-back’s header seemed goalbound but the goalkeeper managed to tip it wide.
Newcastle hadn’t beaten Stoke in five attempts in the Premier League going into this game, losing three and failing to score in four.
That record looked to be changing though, as Lascelles was the hero once more from the corner. Firing home off the underside of the crossbar to give Newcastle the lead.
Lascelles scored the winning goal from a similar position against Swansea last week, and looked to be doing the same thing once again.
Newcastle then looked to see this game off with a third goal, Richie and Ayoze Perez combining down the left-flank to a chorus of cheers from the home fans.
Stoke had a chance to equalise late on, as substitute Peter Crouch found Eric-Maxim Choupo-Moting inside the area but he could not keep his effort down.
Diouf then met a wonderful cross by Bruno Martins Indi, but was only able to head his shot wide as Newcastle held on for the three points.
This result sees the Magpies winning three of their opening five Premier League fixtures for the first time since 2000-01, when they went on to finish 11th.