The Oranje midfielder struggled to contain Die Mannschaft's Bastian Schweinsteiger during the opening 45 minutes in Kharkiv and did not re-emerge the second half
Having failed to disrupt Bastian Schweinsteiger's influence over proceedings and with his side trailing to a Mario Gomez double, the veteran midfielder was hauled off during the interval in Kharkiv and replaced with Rafael van der Vaart.
Van Bommel, though, claimed afterwards that he was not upset by his withdrawal, even though he argued that the switch had not worked, with Netherlands failing to salvage a point despite being given a lifeline by Robin van Persie with 17 minutes to go.
"It's not about who did or did not play," the Oranje skipper told NOS. "It was important that we did not lose the game and you must be subordinate to the needs of the team.
"The coach tried to make an impact on the rest of the game, but it was not enough unfortunately."
Van Bommel admitted that the Dutch only had themselves to blame after affording their opponents too much space and time with which to work.
"Defensively, we were not good enough," the PSV man acknowledged. "We started strongly and created a half-chance.
"But then we gave away two goals, and also a free header for [Holger] Badstuber. That did not put us in a good position for the rest of the game."
In order to progress to the last eight from Group B, Netherlands must now defeat Portugal by two clear goals and hope that Germany beat Denmark.