The 36-year-old's 218th international strike was pivotal, coming just 25 seconds after half-time to give the Netherlands a lead they never let slip.
It leaves defending Olympic champions Germany requiring a point from their final match against New Zealand to join the Netherlands in the last four.
The game had begun well for Germany as Christopher Zeller converted a low penalty corner flick inside two minutes.
Netherlands almost equalised when Billy Bakker's cross-shot only just evaded the sliding De Nooijer at the far post.
That marked a change in momentum and when Valentin Verga's shot was only half-saved by goalkeeper Max Weinhold the ball dropped to Bob de Voogd who swept home from close range.
Germany's only other real chance of the half came when Thilo Stralkowski cut into the top left of the circle only to have his powerful shot parried by goalkeeper Jaap Stockmann.
Netherlands had the final action before the interval when Roderick Weusthof flicked over a penalty corner but just 25 seconds into the second half the crucial breakthrough was made. Zeller gave away possession in midfield and the ball was quickly transferred to De Nooijer who exchanged passes with Bakker, bypassing Maximillian Mueller in the circle, and slid in at the far post to convert.
Soon after penalty corner specialist Mink van der Weerden scored his fifth of the tournament from a well executed set-piece.
Having barely touched the ball in the second half Germany found a response and forced Stockmann into two saves, although neither really extended the goalkeeper.
Zeller's driven pass was deflected goalwards by Jan Philipp Rabente only to be easily stopped before Oskar Deecke's angled effort was palmed aside.
The last 15 minutes saw Germany step up the pressure but that allowed Netherlands to hit them on the counter-attack and defender Martin Haener had to hack clear in front of his own goal to prevent De Nooijer bundling in his second of the game.
Late on a Zeller penalty corner and a snap-shot from Florian Fuchs were easily dealt with by Stockmann as the Netherlands held out for a deserved win.