The Gunners endured a frustrating 70 minutes in North London as PSV absorbed copious amounts of pressure, but Granit Xhaka's smart half-volley in the second half was all that was needed to separate the teams and guarantee a top-two finish for Arsenal.
Within the first few minutes of the contest, Arsenal had PSV exactly where they wanted them; pinned inside their own half and barely getting a sniff in the final third.
However, goalkeeper Walter Benitez remained untroubled in the opening exchanges, as Kieran Tierney fired a volley over the top while Gabriel Jesus and Xhaka both dragged efforts wide.
Ruud van Nistelrooy's side would seldom venture forward, but 19-year-old starlet Xavi Simons did show a glimpse of his potential after driving through a non-existent Arsenal midfield before firing harmlessly over.
A Fabio Vieira free kick just before the break crashed into the side netting as Arsenal re-entered the dressing room having failed to force Benitez into a single save, but that would change early in the second half.
Seven minutes after the restart, a stumbling Jesus managed to get his shot away before losing his footing, but his tame effort was never troubling Benitez, and Bukayo Saka was then denied by the ex-Nice man two minutes later.
Mikel Arteta's side began to up the ante in their quest for a five-point buffer over the Dutch champions, as Jesus and Eddie Nketiah both failed to make the net ripple after driving runs into the centre.
A PSV side who were largely camped inside their own half did force the previously quiet Matt Turner into a save after the hour mark, as the American got down low to prevent Simons finding the far corner.
With the game approaching its final 20 minutes, Arsenal finally made the breakthrough in some style, as Takehiro Tomiyasu's cross from the right found Xhaka unmarked by the penalty box, and the Switzerland captain picked out the corner on the half-volley on his weaker right foot, although the ball may have taken a nick off Andre Ramalho into the back of the net.
Arsenal had their tails up, and Saka nearly doubled Arsenal's lead immediately, as the England winger evaded several PSV challenges in a mazy run before forcing a good save down low from Benitez.
Concern was then raised when Saka went down clutching his calf, but the 21-year-old was fine to carry on and force another save out of Benitez after substitute Gabriel Martinelli had been denied by the Argentine from a tight angle.
Arsenal will now compete in the knockout round playoffs at the very least, and they only need to draw against PSV at Philips Stadion next week to guarantee a first-placed finish in Group A.