The Blues will travel to Spain on Tuesday having spent 124 of their last 210 minutes on the field with a man disadvantage, hardly ideal preparation for what is expected to be the toughest of their Group E assignments.
Alex's dismissal in Wednesday night's Carling Cup penalty shootout win over Fulham and an injury to Daniel Sturridge forced manager Villas-Boas to introduce John Terry and Frank Lampard, who he had been hoping to rest.
That had a knock-on effect for Saturday's 4-1 Premier League victory over Swansea, with Petr Cech the only survivor from the midweek XI, while Lampard was left on the bench to demonstrate that, at 33, he is being held back more and more for the big games.
Villas-Boas was clearly keen to avoid further fatigue but Fernando Torres put paid to that on Saturday when he inexplicably lunged at Mark Gower 10 minutes after opening the scoring with a trademark finish.
His manager played down the impact Chelsea's recent indiscipline might have at the Mestalla.
"It should be okay and nothing to worry about," Villas-Boas said.
"It's also early beginnings in the league."
Yet, the Portuguese conceded the importance of freshening up his side yesterday.
"I think the decisions were mainly based on the fact that we played 120 minutes on Wednesday," he said.
"We sent nine players fresh to the pitch that didn't play on Wednesday and I think this has an impact.
"It's important to have squad rotation."
Ironically, Torres' red card therefore makes him more likely to start on Wednesday as he only played 39 minutes yesterday, was not involved at all against Fulham, and is now banned for the next three Premier League games.
So Didier Drogba's return from a sickening head injury could hardly be more timely, the forward coming off the bench on Saturday to net Chelsea's fourth goal and his first of the season.
Villas-Boas said: "We have four wonderful strikers and all of them have been performing very, very well - Lukaku, Nico, Didier and Fernando.
"All of them compete for a place in this 4-3-3 that we privilege."
He added of Torres' ban: "It will mean opportunities for the other three to challenge for that position."
Drogba claimed last week he was lucky to be alive after being knocked out in Chelsea's win over Norwich four weeks ago.
But he immediately put his head where it hurt yesterday in an aerial challenge with Ashley Williams, who went on to net Swansea's consolation after a Ramires brace.
Villas-Boas said: "After missing so many days through concussion, maybe a different player wouldn't challenge for that ball straight away with that commitment and that drive.
"This represents Didier as a person and as a player."
Swansea boss Brendan Rodgers singled out one of his own players for special praise, despite the worrying manner of Saturday's defeat.
"I thought our young player, Joe Allen, was absolutely outstanding," said Rodgers, whose side's impotence in front of goal returned to compound what was poor defending against 10 men.
"Twenty-one years of age and he showed that he's got a great future ahead of him and great confidence and ability with the ball."
Rodgers was given an ovation before kick-off on his return to the club where he was reserve-team manager for four years.
"It's a very special club," he said in his post-match press conference.
"I used to stand in here many times watching everyone else getting interviewed, trying to learn and progress, and all of a sudden you're sat here.
"The reception, I really appreciate from the Chelsea supporters.
"It's a club that gave me every chance and possibility.
"I wouldn't be a Premier League manager today if it wasn't for them."
Source: Team Talk
Source: Team Talk