Wigan goalkeeper Ali Al-Habsi was a spectator for much of the encounter in north London, and Villas-Boas' men were very fortunate that Ben Watson's strike was the only goal they conceded.
"It was maybe our worst performance of the season," said Villas-Boas, who saw his team booed off against Norwich and West Brom earlier in the campaign.
"We didn't manage to keep the ball or pass well. We couldn't recognise ourselves today.
"Wigan were superior. Our chances weren't clear cut. There are various reasons why we played like this.
"The opponents were sharp and aggressive. We kept making mistakes. We played more with the heart rather than the head."