The hosts had to rely on a last-minute goal from Maroune Fellaini to overcome their dogged Spanish opponents, with Wayne Rooney missing a first-half penalty.
Darren Fletcher put United ahead soon after the restart, only for Rodrigo Moreno to level matters after capitalising on a poor attempted clearance by Tom Cleverley.
And Van Gaal was not impressed by his side's showing ahead of their Premier League kick-off against Swansea city on Saturday.
"I think it was our worst match to date," he told MUTV. "The boys wanted to show the capacity we showed in the United States perhaps a bit too much. There were a lot of wrong passes, wrong choices and we didn't press so well.
"But, in spite of that, I think Valencia are a very good team, very comfortable on the ball, so it's not so easy to press. In spite of that, we have dominated the game - only for 15 minutes in the second half we weren't dominating. In the end, we were the winners because we were fighting until the last minute. That's a good signal, I believe.
"At this moment, we are fitter than our opponent," he declared. "You could see that. But it was also the changes. Fellaini and Januzaj have only been with us training for one week. They can't play any more minutes than they did tonight.
"I had a lot of young players. They did reasonably well but they could do better, I believe. But it's a start. It's not easy to play at Old Trafford for the first time so I'm pleased we've won the game against a very good team. Of course, I think we have to make better choices with our passing - we didn't do that and that's a pity.
On his first game at Old Trafford, Van Gaal added: "I enjoyed it. Coming onto the pitch, the fans are shouting and screaming your name. It's also a big pressure.
"They expect a lot and you can't change everything in three or four weeks. And the players can't change either. We have to wait and see and develop. We need time but we have won every game up until now and that's fantastic when you see our opponents. We have great confidence to play against Swansea City."
Jonny Evans, Luke Shaw and Antonio Valencia all sat out the game as they continue to struggle for fitness ahead of the new season, and Van Gaal was coy when questioned on their respective bids to face Garry Monk's side.
He added: "We have a lot of injuries now. Don't forget, Jonny Evans was injured, Luke Shaw was injured, Antonio Valencia was injured. These are three defenders. We have to wait to see if they can play on Saturday. The main thing is that we have won, despite playing our worst game."