With manager Peter Bosz resting key players such as Noa Lang and Ismael Saibari for the Champions League away game at Red Star Belgrade, Guus Til and Ivan Perisic got the nod for the second game running after their starts in the cup game against Excelsior (5-4 win).
A rough start meant PSV fell behind after just two minutes when Bulgarian winger Filip Krastev opened the scoring for the home side with a great effort from distance.
Unable to successfully find their way through PEC's defense in the opening stages, PSV squandered an opportunity ten minutes after Krastev's opening goal when Jokan Bakayoko couldn't manage to hit the target after a cross from Perisic.
That same duo struck again 25 minutes in and put PSV alongside PEC when Bakayoko got on the end of a driven pass from Perisic and fired home for the 2-1.
PSV, who drew at home to AZ last week, finally got things going and earned a penalty when Eliano Reijnders kicked Perisic in the calf and got punished for it after a VAR check. Luuk de Jong took the penalty, but failed to score in his third consecutive game after he put the penalty wide left.
Things got from bad to worse for PSV when Krastev added a second goal to his tally after the Bulgarian picked up a loose ball from a corner and fired it past Argentinian goalkeeper Walter Benitez for PEC's second lead of the day.
PSV managed to create several opportunities after the break and kept PEC at bay, but hardly managed to put PEC goalkeeper Mike Hauptmeijer in jeopardy.
Shortly after substitute Noa Lang got things going up front and created a chance for fellow substitute Ricardo Pepi, PEC thought they'd hit once again when Nick Fichtinger headed in a corner just one minute after coming on. The home fans were however left disappointed after referee Jeroen Manschot disallowed the goal after Dylan Mbayo was deemed to be offside.
A faltering PSV still conceded a third after Filip Krastev escaped from the defence and was allowed to run freely at the league leaders' goal with Dylan Vente alongside him before passing the ball to Vente and adding an assist to his two goals.
PEC Zwolle earned a hard-fought victory in their battle against relegation and won their first game since November, a game which moves them up to thirteenth in the Eredivisie.
PSV could see rivals Ajax and FC Utrecht close the gap to respectively one and four points after their games against Heerenveen and AZ.