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 night.
Chelsea went out of the Champions League on Wednesday 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, said: "I think it's extremely unfair. 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."
He went on: "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."
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.
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.
The Spurs boss said: "Sometimes it's destiny. Hopefully if we go through we can meet each other."
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 Tottenham only sealed victory thanks to a late own goal and Jermain Defoe's chipped strike.
"Panathinaikos put in a good performance, they were very well organised," Villas-Boas said.
"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."