Chelsea striker Didier Drogba
Goals from David Luiz, Didier Drogba and the recalled Frank Lampard were enough to move Chelsea above Arsenal and into fourth place, the final Champions League qualification slot.
The result also left Bolton in the relegation zone as Chelsea owner Roman Abramovich watched from the stands.
Villas-Boas had been forced to admit his team selection for the 3-1 defeat at Napoli in the Champions League on Tuesday night had left him open to plenty of criticism.
Abramovich had demanded an explanation after Lampard and Ashley Cole were left out of the starting line-up, which had not been popular with the majority of supporters either.
Both England internationals were recalled for this game, as was Michael Essien, and defender Gary Cahill started against the club that had sold him in January.
Drogba was also picked to lead the front line, which meant Fernando Torres, who had been omitted from the most recent Spain squad, had to be content with a place on the bench.
Bolton manager Owen Coyle made one change with Darren Pratley replacing Mark Davies in midfield.
Chelsea dominated the first half without being able to get the better of Adam Bogdan, the goalkeeper who had been so poor when Chelsea had won 5-1 at the Reebok Stadium in October.
Bogdan's save to deny Daniel Sturridge early on was not too convincing as he let go of the ball before retrieving.
But he did well to hold up Lampard after the midfielder had burst into the box and, having ridden a tackle, tried to take the ball round the Hungarian.
A defender got in the way of that one and that was also the case when Chelsea forced a number of set-pieces.
There was nothing sub-standard about Bogdan's save to deny Sturridge, who had cut in from the right to unleash a low drive.
Drogba was full of invention and intention and the Bolton backline had great difficulty keeping him at bay.
They were grateful therefore to Branislav Ivanovic for effectively tackling his team-mate when Drogba was just about to shoot.
The half ended with Pratley booked for a dive as he tried to win a penalty as Essien challenged and Ryo Miyaichi, the on-loan Arsenal midfielder, firing just over from a good position in stoppage time.
Chelsea needed just two second half minutes to take the lead however and it was defender Luiz who scored it.
The Brazil international had been involved in the build-up and when the ball broke to him in the Bolton penalty area he cut inside neatly before firing past Bogdan.
Nigel Reo-Coker might have equalised soon afterwards but was unable to hit the target from the edge of the Chelsea penalty area.
Luiz almost made him pay for that miss by getting on the end of Juan Mata's corner delivery to the far post but a combination of Bogdan and Miyaichi saw the ball deflected behind for a corner.
A second goal was coming though and Drogba was the man who scored it just after the hour mark, nodding home a Lampard corner. Miyaichi was perfectly positioned on the line once more to stop it but could not.
Drogba took a knock and was replaced by Torres with 14 minutes remaining.
Lampard made it 3-0 after Mata had picked him out at the back post, with the midfielder's run having not been picked up by the Bolton defence.
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