It was the The Magpies that dominated the first period in terms of chances with good chances from Christian Atsu and Ciaran Clark but to no avail, Stoke picked up the pace in the second period with a chance from Eric Maxim Choupo-Moting but Pérez's strike combined with heroics from Karl Darlow saw The Magpies head back to Tyneside with the three points.
Testing the waters
The atmosphere at the Bet 365 Stadium had began to become toxic over the last few weeks and months with Stoke's performances on the pitch and blame being placed at the feet of Hughes, the Welshman took a gamble by resting players for the 5-0 defeat to Chelsea for this clash in the hope to turn the tide.
However it was The Magpies that started well with a good chance 13 minutes in, Pérez started the move with his change of pace before releasing DeAndre Yedlin down the right. The American cut it back to Atsu 15 yards out but it was straight at Jack Butland.
They had another good chance on the half-hour mark as Jonjo Shelvey sent a corner into the near post which was cleverly flicked on by Pérez, it reached the onrushing Clark who couldn't miss from three yards out but somehow managed to balloon it over crossbar.
Looking for that bit of quality
Stoke did pick up their own pace in the second period with Hughes only having 45 minutes to possibly save his job, but they could only muster the one chance as Choupo-Moting drifted into the space and his effort looked destined for the top corner but Darlow did well to flick it over the crossbar.
Shelvey went close to an opener in the 67th minute as the midfielder faked his free-kick to go over the wall, but he hit it over the other side and just skimmed the corner of the crossbar and post.
Making that crucial difference
The clash was crying out for a moment of magic and it was Rafael Benítez's side that took a somewhat deserved lead 17 minutes from the end.
Jacob Murphy did well to start the move as he accelerated down the right-hand side and fizzed a great ball into the middle, it was perfect for Pérez who was waiting in the middle to turn home despite a touch from Butland.
Coming to the rescue
That seemed to kick The Potters into gear as they looked to take something from the game, but the heroics of Darlow made sure United where heading back to Tyneside with all three points.
His first save came ten minutes from the end as the ball dropped to Mame Biram Diouf eight yards out, and looked to have turned it towards the corner but Darlow did well with the one-handed save to keep it out.
The best was yet to come six minutes later as Peter Crouch did well to turn a cross in from the left back across goal, Diouf came in with the diving header but the goalkeeper did well to scramble it away and Sadio Berhaino couldn't turn the rebound home.