Lively duo Cody Gakpo and Xavi Simmons were kept scoreless in the first half as Arsenal struggled, but PSV finally took the lead when Wirmann headed into the top right corner after the break.
De Jong was outstanding after his introduction at half-time and he scored after beating Aaron Ramsdale and slotting home a corner as Arsenal collapsed.
As a result, PSV secured a place in the knockout stage and also kept their chances of usurping Arsenal for the top spot.
Arsenal were alerted to PSV’s intentions when Gakpo brought down Ramsdale sharply in the 18th minute, only to have it ruled out for offside.
The uninspired Gunners needed another reprieve as the break approached.
Simons somehow wriggled his way through several challenges before slotting past Ramsdale, but a VAR review spotted offside in the build-up to halt the home side’s celebrations.
However, Arsenal’s luck finally ran out nine minutes after the restart when Wirmann took advantage of De Jong’s fine late play to slot home with his left foot.
Mikel Arteta’s side struggled to deal with De Jong throughout the second half and he made sure of the points by beating Ramsdale in a Gakpo corner with a firm header shortly after the hour mark.
Gakpo saw another goal ruled out for offside and De Jong went close with two more headers, but PSV still cruised to victory.