Spurs dropped to fourth in the Barclays Premier League thanks to a Dimitar Berbatov strike which rounded off a poor week for the north London club.
Tottenham, who lost to Liverpool last Sunday and Inter Milan on Thursday, are four points ahead of Arsenal, who have a match in hand, against Everton next month.
Spurs threw away Champions League qualification last term thanks to a woeful run in the final quarter, but Villas-Boas is adamant that will not be the case this time around.
The Portuguese claims that so long as Spurs pick up good results against rivals Chelsea, Manchester City and Everton in the run-in, then they will qualify for Europe's top club competition.
"The situation has shifted, it has become difficult," the Tottenham manager said.
"We have the direct games against Arsenal and Chelsea which can enable us to get back to third hopefully, or bring Man City closer to us.
"The margin over Arsenal is what we want to build and we have to get the most amount of points from the next games.
"After the international break we have to get back to business and do our job against Swansea and try to collect the points there to put us in a more comfortable position by the time we play Man City."
Tottenham offered little on Saturday to suggest Villas-Boas would be right. Their passing was sloppy, their defence shaky, and Cottagers goalkeeper Mark Schwarzer was only called into action late in the second half.
Fulham manager Martin Jol, who tasted victory at White Hart Lane for the first time since he was sacked from the north London club in 2007, hailed Berbatov after the game.
The Bulgarian has now racked up 10 goals this season, and he was so confident that he would secure a shock victory for the west London club that he told his manager he would do so before the match.
Jol said: "Before the game you hope for a point... but Berbatov came to me and promised me... He said: 'you have to trust me'.
"I thought he was joking. But he said it before the match against Stoke (where he scored the winner) and he is a wonderful player.
"It was one of the best wins ever."
Tottenham forward Gareth Bale, meanwhile, took a knock to his right ankle but should be fit for international duty with Wales this week.
Villas-Boas has ruled Aaron Lennon (groin and hamstring) and Michael Dawson (hamstring) out of England's double-header with San Marino and Montenegro, though.