The 2010 World Cup finalists were three minutes away from winning on the road after new Roma signing Kevin Strootman gave them the lead in the 17th minute but a Cristiano Ronaldo strike ensured the friendly finished 1-1.
Van Gaal acknowledged that a draw was still a good result but questioned his side's fitness and composure in the second half, believing that his players ran out of steam in the encounter.
"In the first half we created as many chances as Portugal did," Van Gaal said. "We created a goal and I cannot say anything [bad] about the first half.
"If you do not lose against teams like Germany, Italy and Portugal, you are doing it right, but after the break we had possession and played very badly.
"We could not hold the ball and we saw the energy running out with some of the guys."
Netherlands have not lost a match since August last year and look set to qualify for World Cup 2014 as they have won six times in as many qualifying matches.