Spurs welcome Basel to White Hart Lane for the opening leg of their quarter-final tie and the Barclays Premier League club have been labelled as favourites to progress to the final four.
Reigning Swiss Super League champions Basel have beaten the likes of Manchester United, Bayern Munich and Sporting Lisbon over the past two seasons - reaching the knockout phases of last year's Champions League in the process.
That recent record means Villas-Boas is taking nothing for granted as he looks to lead Spurs to their first piece of silverware since the League Cup triumph of 2008.
"Obviously they have recent European experience that we don't have," he said.
"They have got tremendous results in the past year with Man United and teams like Bayern - teams they have surprised. They are extremely successful and one of the best teams in the country.
"I'm sure that the key to the game will be both team's motivations and the quality of the individuals - we have to admit that we have superior players but, on the other hand, the experience Basel have and the fact they have played in the Champions League and are regular trophy winners, makes them also one of the favourites."
Tottenham sit third in the Premier League, with Champions League qualification part of Villas-Boas' remit when he replaced Harry Redknapp at the helm last summer.
The Portuguese admits securing a top-four finish is important but pointed towards former club Chelsea as an example of a team who have won silverware after missing out on the Champions League places.
"We want to focus on trying to win the Europa League but we understand that the fans' and the club's expectations are for us to try and reach Champions League qualification this year," he said.
"What sets the success of a football team is their league position at the end of every season but we want to do extremely well in the competition.
"It would be very, very important for us to get a trophy this season and I think we have taken great steps towards the future by the way we have embraced this competition.
"We were rewarded with two great opponents [Inter Milan and Lyon] who are full of Champions League experience and Basel is another one.
"I think it always dictates the success of a season, your league position, but winning a trophy is always important.
"Chelsea finished sixth last season but it was completely overshadowed by the fact they won two major competitions and the most important competition in the world - it was deemed a successful season in the end."
Tottenham's task of securing a healthy first-leg lead have been dented with the news that England striker Jermain Defoe will miss the game through injury.
It is believed Defoe will not be missing for more than 10 days but the second leg in Switzerland next week could come too soon for the 30-year-old.
"Jermain has a muscle injury that is probably going to take him out of the next two games and maybe Basel away," Villas-Boas said.
"If he can't make Basel away he should be fit in the week when we prepare to play Manchester City.
"It is a big blow, it is on the muscle he had a small tear last month but it is on the other side now. He is a big miss and has shown tremendous quality this season."
Goalkeeper Hugo Lloris has recovered from the knee problem that saw him miss Saturday's 2-1 win over Swansea and will be a part of the squad but, with Brad Friedel the preferred option in the Europa League, the France captain is likely to be among the substitutes on Thursday night.