Ben Watson's goal gave Wigan a shock 1-0 victory at White Hart Lane to condemn Spurs to their second straight home defeat.
Spurs were booed off by their supporters after the game and Villas-Boas had no complaints with the result, admitting that Wigan were the better side and deserved the three points.
"I think they were the better team today," said Villas-Boas. "They were extremely well organised and I think credit to them for the difficulties they created for us.
"For sure it was our worst performance of the season. I think we have the right to have a bad day in the office and I think today was an example of that.
"Credit to the opponent, we had difficulties because we were always under pressure. They managed to organise themselves very, very well and were aggressive in recovery of the ball.
"We went through the first half where we did not have any chances at the goal and they had two good chances to go ahead before us.
"They were superior during the 90 minutes and we make a reflection on the mistakes we did as it is very important if you want to move on in the future."