The Portuguese left Ashley Cole, Michael Essien, Frank Lampard and Fernando Torres out of his starting XI.
"You can have your opinion but it was based on what was the best team in my thoughts," he said.
"We will analyse strongly what we did wrongly because a couple of things need to get better. It is not impossible to recover from 3-1."
Cole was introduced as a 12th-minute substitute for the injured Jose Bosingwa, who started at left-back despite Cole having more than 200 starts for Chelsea and 93 England caps in the position.
Essien and Lampard came off the bench in the second half with their side two goals adrift.
VILLAS-BOAS AT CHELSEA
Win percentage: 45%
"I had a conversation with Ashley and Frank. Through the players that they are and the players with the experience they have, they felt they could have helped the team," added Villas-Boas.
"That's perfectly understandable."
With Chelsea 17 points off the top of the Premier League and facing a tricky FA Cup fifth-round replay away to Birmingham on 6 March, the Champions League could be the only trophy which the west Londoners still have an interest in by the time of the second leg on 14 March.
Villas-Boas insisted that despite his side's failure to win any of their past five matches, he was confident he would still be in charge when that game is played.
Graham TaylorExpert Summariser
"Napoli have edged this game deservedly, but I still don't rule out Chelsea going through at Stamford Bridge. I don't think it's over yet but defensively Chelsea have to get better."
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.