With Arsenal safely through, manager Mikel Arteta rang the changes with just William Saliba, Gabriel and Kai Havertz retaining their places in the starting XI.
That may have played a role in their sluggish start, with PSV much more lively in the opening stages.
The Dutch side’s only defeat this season was the 4-0 loss at Emirates Stadium, and they played with freedom and confidence.
Aaron Ramsdale – one of the eight Arsenal changes in his Champions League debut – saved well from Saibari before USA striker Ricardo Pepi struck the post with a header.
Arsenal held out and took the lead through Eddie Nketiah, in a much-needed riposte to critics of his place as a striker at Champions League level.
But their poor recent history in the Netherlands continues. Arsenal have now failed to win in their past four European visits to Dutch sides since a 2-1 Champions League victory at Ajax in September 2005.