Spurs missed the chance to cement their bid for a top four Premier League finish after slipping to defeat courtesy of Dimitar Berbatov's goal against his old club.
Villas-Boas admits it was a bad day at the office for Tottenham and conceded Fulham deserved to take all three points.
"It was difficult and it is two defeats in a row in the Premier League and we wanted to avoid that because we were on a good run," Villas-Boas told Sky Sports.
"We had a decent game, but we couldn't create as much as we normally create at home offensively.
"So our main chances were at the beginning in the first half and late in the second half, but we couldn't create as much as wanted to to take the win.
"It was one of those defeats we have to reflect on. The desire and effort was there, but things just didn't go our way in terms of football."
Asked if fatigue was a reason for Tottenham's below-par performance, Villas-Boas said: "No. We played lots of players who were not involved recently and had a couple of fresh legs on the pitch - five at least."
Mark Schwarzer denied Jermain Defoe late on with a stunning late save and Villas-Boas admitted the keeper did well to deny the striker.
"Towards the later stages of the game we had opportunities with Defoe and if we could got the equaliser we could have pushed for a winner, but Schwarzer did ever so well to deny Defoe and Fulham deserved to win," concluded Villas-Boas.