Newcastle continued to create chances in the second half with midfielder Jacob Murphy charging past the tiring Stoke defenders in the 73rd minute to feed the ball to the oncoming Perez, with the Spaniard making a cool finish to seal the win.
Stoke piled on the pressure in search of an equaliser but were kept at bay by Newcastle goalkeeper Karl Darlow, who made several impressive saves to condemn the Potters to a second successive defeat.
Stoke boss Mark Hughes was booed off the pitch after the match and is on the brink of being sacked with the club recording just five wins in 22 league games this season to slip to 16th in the rankings.
"We didn't deserve to lose. But their keeper made some great saves," Hughes said.
The Welshman was criticised as Stoke were thrashed by champions Chelsea last week after resting key players with the Newcastle game in mind and the 54-year-old made six changes to his side on Monday, to no avail.
"Everybody talks about the changes we made but (Newcastle manager) Rafa Benitez made six changes, what's the difference. I don't see why my decisions are questioned. I am brave enough to take it on the chin," Hughes added.
Stoke have conceded 47 goals, the most in the league, and sit just two points above the relegation zone having played two more games than 18th-placed West Ham United. Newcastle climb to 13th after a much-needed win.
"Today we had chances, we scored the winning goal and it will give us confidence. The team is focused and there is a long way to go," Newcastle boss Rafa Benitez told reporters.
(Reporting by Aditi Prakash in Bengaluru; Editing by Christian Radnedge)
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