The Blues won the game 3-0 to book their place in the final 16 of the prestigious European competition, with Lampard the only player to lose his place in side following the Premier League win over Newcastle last Saturday.
Lampard was an unused substitute on Tuesday, but the Portuguese manager insists the England midfielder is in contention to face Premier League leaders Manchester City on Monday.
"Frank has been fantastic. We have to select 11 and he wasn't in this 11," Villas-Boas told BBC Sport.
"Important players have been left out at Chelsea, players of immense talent."
Villas-Boas opted to use Raul Meireles, Ramires and Oriol Romeu in midfield against the Primera Division side, but insists this was purely tactical and not down to Lampard's technical ability.
"He has been in a fantastic moment and is sure to threaten for the starting XI on Monday.
"He is one of the greatest players in the world but this choice was three players in midfield because of their technical ability to keep possession and keep it on the ground without a lot of long balls.
"We know that Frank can also do this but he was not our choice for this game.
"He will come back in the future certainly. He has been fantastic in the way he has taken these tough decisions."
The Blues boss also kept faith in another of Chelsea’s more experienced players, Didier Drogba, who proved his worth by netting two goals and setting up the other for Ramires.
The Ivorian added: “There was a lot of pressure but, when you start the group stage, you know you have to play until the last day.
"We had a chance to finish top of the group and our attitude was positive. We wanted to get the result. The pressure can sometimes be positive and it was in this game."
With the striker continually linked with a move away from Stamford Bridge in recent weeks, the former Marseille forward insisted the team's performance this season was more important than his own future.
"My future is not important. The most important thing is to put the team back in the position we want to be in, at the top of the Premier League.
"We are not happy where we are now."
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