The England duo were left out from the start with Cole replacing the injured Jose Bosingwa after just 10 minutes and Lampard coming on for Florent Malouda with 20 minutes to go.
"We wanted two hard-working midfielders sitting in front of the defense. That's not to say that Lamps could not do it, for sure he could, but that was the decision we took," Vilas-Boas told reporters.
Villas-Boas’ decision was not vindicated as Ezequiel Lavezzi's double and a Edinson Cavani strike helped the Italian outfit to a 3-1 victory.
And the Portuguese boss says he understands why Cole and Lampard were upset but claims it is useless making excuses following the bad result.
"Whatever explanations I gave you would be fantastic if we'd won but are now useless given the result of the game, so there's no point," he said.
"It was technical decisions. You can have your opinion but it was based on what was the best team in my thoughts."
He added,"I had a conversation with Ashley and Frank. Normally, through the players that they are and the players with the experience they have, they felt they could have helped the team.
"That's perfectly understandable. Of course, they were disappointed but they were decisions they have to accept and move on."
The defeat leaves Chelsea staring down the barrel of elimination from the competition which owner Roman Abramovich is known to most covet.
Villas-Boas bemoaned his side’s lack of quality in front of goal but says they can turn things around at Stamford Bridge on March 14.
"In this game the difference was that Napoli were more clinical and efficient in front of goal," he added.
"We have big chances and paid a heavy toll for the mistakes we made but I am sure we can turn it around."