Spurs booked their place in the last 32 of the competition with a nervy 3-1 win over Panathinaikos at White Hart Lane on Thursday.
Having finished second in Group J, Tottenham will not be seeded in the second round of the competition, meaning they could face Benfica, Olympiacos or CFR Cluj, who drop in to the draw having been eliminated from the Champions League after finishing third in their respective groups.
Chelsea went out of the Champions League despite winning 6-1 against Nordsjaelland last night, but Villas-Boas will not be able to take on his former club until the next round as teams from the same country cannot face each other until the third round.
Villas-Boas, who won the competition with FC Porto in 2010, thinks it is unfair that the Blues, and the rest of the Champions League drop-outs, are allowed in to the tournament.
"I think it's extremely unfair," the Tottenham boss said.
"It would be much fairer if the clubs came in to the Europa League when they are knocked out of the last 16 of the Champions League.
"You can't give a bonus to teams who have failed, and in the situation as it stands, teams fail in the Champions League and are promoted to the Europa League, which, in my opinion, is a massive bonus.
"I've not made this up today. I have said this in UEFA meetings before. It's up to them to decide but I think it's not fair."
Villas-Boas took Chelsea through to the second round of the Champions League before he was sacked following the club's first leg defeat to Napoli. He lasted just over eight months in the job.
The west London club then went on to win the tie before lifting the Champions League for the first time in their history under Roberto Di Matteo.
Villas-Boas admitted he felt let down by the club's owner Roman Abramovich after his sacking and he thinks destiny could pit the two London clubs against each other in the last 16 of the competition should Spurs win beat their next opponents.
"Sometimes it's destiny. Hopefully if we go through we can meet each other," said Villas-Boas, who will learn who his team plays next on December 20.
"They have a team that can win the trophy, so they will be up to the late stages of the competition. We hope to do so. If we cross it is going to be two magnificent games for sure."
Having won their last three Barclays Premier League matches, Tottenham were big favourites to beat Panathinaikos, who went in to the match without a win against a British side.
The Greeks played the better football in the first half, however, and despite Emmanuel Adebayor's 29th-minute opener, Tottenham looked nervous.
Zeca pulled Pana level just after the break and Spurs had to withstand some heavy pressure before Jermain Defoe and an own goal from Orestis Karnezis eased the tense atmosphere inside White Hart Lane.
"Panathinaikos put in a good performance, they were very well organised," Villas-Boas said.
"When they equalised it brought a bit more emotion into the game.
"They had a big chance at 1-1, but it would've been unfair if we had lost. It was a good solid performance during the 90 minutes. We managed to hold on and score which was important for us."
Panathinaikos coach Juan Roman Rocha was proud of his players despite their elimination from the competition.
He said: "It was a good performance. We had some hope but it was always going to be a very difficult game against Tottenham. They are one of the Premier League challengers.
"Maybe we could have nicked it but in the end we cannot dwell on the past, it is finished and we have to look forward to the next game."