Lampard, 33, who has played in more than 500 matches for Chelsea since joining from West Ham United 10 years ago, was an unused substitute as Villas-Boas opted for a midfield three of Oriol Romeu, Raul Meireles and Ramires against the Spanish team at Stamford Bridge.
However, Villas-Boas, who also took Lampard off during Saturday's 3-0 Premier League win at Newcastle United, said he was in contention to face Premier League leaders Manchester City at Stamford Bridge on Monday.
"Frank has been fantastic. We have to select 11 and he wasn't in this 11," Villas-Boas said. "Important players have been left out at Chelsea, players of immense talent.
"He has been in a fantastic moment and is sure to threaten for the starting 11 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 certainly come back in the future. He has been fantastic in the way he has taken these tough decisions."
SLAP IN THE FACE
Chelsea, who could have missed out on qualification for the knockout stages, won easily on Tuesday to top the group with two goals from experienced striker Didier Drogba, who also set up a goal for Ramires.
"Finishing top of the group is fantastic," Villa Boas said. "It is against all odds. Nobody would have put a bet on us finishing top but it has happened and it is very satisfying.
"The team was excellent. It was a win of human values, team spirit, solidarity, responsibility, strength of character, resilience, ability to take criticism."
Although Villas-Boas was delighted to top the group, which means they will avoid Spanish heavyweights Barcelona and Real Madrid in the last 16 draw, he could not resist hitting back at the media who had criticised him in recent weeks after they had lost three of four matches.
"We've been chased by different kinds of people and pressures. Here we have given everyone a slap in the face," the Portuguese said.
"It is unfortunate for you guys because you have to report on a brilliant win for Chelsea. "It [the coverage] has been over the top."
Villas Boas said he had been particularly upset by the criticism from former Manchester United and England defender Gary Neville, now a television pundit.
"We see a "Manchester United" defender [Neville] say in the preparations for the game things like, 'I don't want to be one of the Chelsea players today, I couldn't play this game and it is a difficult game for them'.
"This is out of this world for me, I don't believe this. This is a continuous persecution, it is aggression towards one club."
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