The Dutch side struck early through Luuk de Jong's second-minute goal, but a pair of late finishes from Harry Kane sealed the win for Spurs.
On Monday, the pitch passed pre-match inspections, but was not up to Van Bommel's liking as he called the field "outright disturbing".
That message carried through on Tuesday, although he admitted his side didn't lose just because of the pitch issues.
"It's s***," the manager said of the pitch at his press conference following the loss.
"It's bad. It's not good but we aren't complaining. I told the guys after a minute, 'Stop complaining and go and get used to the pitch'.
"Everyone wants a good pitch but you have to deal with it."
It's not the first time the Wembley pitch has come under fire in recent weeks as a clash between Tottenham and Manchester City featured NFL lines and less-than-stellar grass conditions following an American football game in London.
The field will next be used by England on November 15 for a match against the U.S., while Tottenham do not play at home until November 24 against Chelsea following a visit to Crystal Palace this weekend.
With Tuesday's win, Spurs kept their hopes of progressing to the knockout round alive but need results against Inter and Barcelona if they hope to pull off a miracle push to the next stage of the Champions League.