Van Gaal's men, who lead their FIFA World Cup qualifying group by six points from Romania following the setback, looked to be on their way to victory when Arjen Robben netted after just two minutes.
However, two goals from Konstantin Vassiljev turned things around for the hosts and put them on the brink of a shock victory.
Manchester United striker Robin van Persie spared Netherlands blushes, though, as he found the net from the penalty spot in injury time.
Still, Van Gaal was left disappointed by his side's negative reaction following the equaliser.
"We played a good first half and created good situations from possession," Van Gaal told SBS6.
"We gave away no chances and made it 1-0 straight away. There seemed to be nothing to worry about.
"But when they had not even had a chance they made it 1-1, thereby tilting the game.
"The confidence was gone. We weren't able to get it back and dared not to build more (attacks)."
However, Van Gaal did praise the spirit of his side after snatching a point in the dying stages, although he conceded it was far from an acceptable display.
"I'm glad we had the spirit to come back," Van Gaal said.
"Fortunately we got a penalty and we were able to get back to 2-2.
"You can't be satisfied with that but I have the ambition to go to the World Cup with this group.
"(They are) players who want to go through the fire for me."
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