The United boss slammed the Premier League fixture list ahead of a trip to White Hart Lane, which came two days after Boxing Day's 3-1 home win over Newcastle United.
Van Gaal's men caused Tottenham all sorts of problems in the first half, but a combination of poor finishing and fine goalkeeping from Hugo Lloris ensured they were unable to open the scoring.
Tottenham improved after the break and United also had their chances, but had to settle for a draw which stretched their unbeaten run to nine matches.
Former Netherlands coach Van Gaal was in no doubt that a traditionally hectic schedule was to blame for United's second-half showing.
He said: "I have said already, one month ago, what I think about this. It's scientifically proven that the body cannot recover within 48 hours.
"When you as an FA allow that to play matches, you see what it's like. The second half much different to the first half. And not only for Manchester United, also for Tottenham Hotspur because I think Tottenham Hotspur can play much better than today.
"And also my team could have played in the second half much better. But you cannot do that and also my colleague [Mauricio] Pochettino has changed three players. It's not for nothing."
United will head into their New Year's Day encounter at Stoke City third in the table and Van Gaal is confident there is more to come from his side in the second half of the season.
He said: "Of course, of course, of course. We shall be better [than the first half of the season]. So watch."
