A majestic goal in the 73rd minute from Robin van Persie gave the Dutch a fighting chance in the latter stages but they looked physically spent having been forced to chase the game after falling behind.
Joachim Low's Germany will qualify as group winners if they draw or win their final match against Denmark in Lviv and they are shaping up nicely for a push for a fourth European title.
The mathematics may not yet be clear but what was certainly decided in the humid heat of the Metalist Stadium was that the Germans and not the Dutch are the real challengers to Spain's crown.
"It was supposed to be our night but we ended empty-handed as we played poorly," was winger Arjen Robben's frank assessment.
"There is no cohesion between our lines, there are gaps and we are not connecting and then it is very difficult to recover the ball," he added.
The early indications were, however, that the Dutch were going to give Germany's back line a torrid test and skipper Mark van Bommel sent Van Persie clear but he was unable to beat goalkeeper Manuel Neuer.
That chance triggered an instant reaction from Germany with Mesut Ozil's volley rattling the foot of the post and the ball rolling into Dutch keeper Maarten Stekelenburg's hands.
"I felt around 65-70 minutes the Dutch were physically drained, very tired," said Low.
"We could have tied it up earlier in the second half. I thought they were tired and we could get a third goal but then it got a bit more exciting with Van Persies's goal," he added.
The Netherlands' problems in their opening defeat by Denmark were limited to a misfiring attack but Van Marwijk said the weaknesses spread much deeper against the Germans.
"In defence and midfield, we gave too much space for them and there was maybe a lack of courage, there was no initiative there," he said.
