Terry blow means defence must be 'reorganised'
Chelsea will have to try to turn that deficit around at Stamford Bridge in three weeks' time but to have any chance of doing so they would probably need to keep a clean sheet, something which doesn't look likely without Terry.
Defensive midfielder Raul Meireles was at fault for the first goal, right-back Bransilav Ivanovic was out of position for the second and Luiz made a howler for the third.
"We have to focus on reorganising this relationship between this back four that we have recently used," said Villas-Boas, who will find himself increasingly under pressure in the unforgiving English press this week.
"I have to agree that you have to solve the mistakes which you do at the back so you can profit better from the number of opportunities you have and the goals you score.
"We need to get this concentration right and this efficiency right that's for sure.
"Without John we were missing a very important player for the team.
"We have fit players and we have to continue to work with them to get it right.
"The first two Napoli goals we had more numbers and we were more organised and if we can concentrate more we can avoid conceding those."
As for Terry, the Portuguese boss is hoping his absence will be only for a month but admits it will likely be longer.
That means he is set to miss the return leg and a crucial chunk of the season, including their FA Cup fifth round replay away to Birmingham City.
"Four weeks would be excellent, we'll have to wait to see how the operation goes and hope the player can return within that frame of time but normally it's for six weeks," said Villas-Boas.
It means that young Brazilian Luiz, so composed on the ball but often lacking in focus and concentration when performing defensive duties, will continue in the heart of defence.
Villas-Boas insists he has faith in his player, despite the press critcism of his performances.
"That player becomes a target but if you suffer three goals you can (all) do much better," the Chelsea boss said.
"We'll assess the mistakes and try to correct them, he's a fantastic young player, he's got a great future ahead of him and we have to continue to work on him to improve.
England's Ashley Cole was also overlooked at left-back on his return from injury, although he came on after just 12 minutes due to an injury to Jose Bosingwa.
"It's technical decisions, whatever explanation that I give you in the end it would be a fantastic explanation if we win the game," said Villas-Boas in defence.
"Any explanation I give you is useless with regard to the result of the game, there's no point.
"Regarding the formation with the two sitting midfielders we chose tonight was to have two hard working midfielders to sit in front of the defence, not that Lamps can't do it, for sure he can but that's not the decision we took."
As for his own future Villas-Boas was adamant that he will keep going whatever is written about him.
"Speculation will continue as results don't happen but it won't be a distraction."
Related Chelsea News