The Eagles' return to the Barclays Premier League was settled when debutant Roberto Soldado opened his account for Tottenham with a second-half penalty.
Palace boss Ian Holloway took issue with Clattenburg's decision to award a spot-kick after Dean Moxey handled Aaron Lennon's cross with an outstretched arm in the 50th minute, but Villas-Boas felt it was the correct call.
"I have been told it was clear cut, although I haven't seen it again. People tell me that just before that shout there was one on Paulinho as well so that's the information I have - that his arm was stuck out," said Villas-Boas.
"Although it doesn't look deliberate his arm is quite some distance from the ball. The referee decided wisely."
Villas-Boas refused to comment on the future of Real Madrid target Gareth Bale, but revealed that the foot injury that forced the Wales winger to miss Sunday's victory will side line him for two further matches.
The Portuguese stated that Spurs may buy a defender before transfer deadline day and was pleased with the performance of new signings Soldado, Paulinho and Chadli.
"Bearing in mind that for all of them the Premier League is a different proposition in terms of intensity and passion, I think they did extremely well so I am extremely pleased with that," he said.