The Blues were aided by a penalty in the first half from Eden Hazard, which saw a red card come out for Rashad Sadygov, whilst a brace from Willian in both halves and a Cesc Fàbregas penalty in the second secure their place in the knock-out stages.
Chelsea will have been looking for a positive reaction in the tournament after they were embarrassed last time out in Rome when they were beaten 3-0 by AS Roma and they duly delivered.
The Stamford Bridge outfit started off slowly – which could be due to the 2,500-mile trip they had to make – with Michel hitting the post in the opening 15 minutes, however the Londoners then stepped it up a gear and never looked back.
Hazard played a ball through to Willian who was tripped in the box by captain Sadygov and earned himself a straight red card, leaving the Azerbaijan side to play 70 minutes with ten men.
Once the protests about the dismissal had ended, Hazard stepped up to take the penalty cooly and slotted it into the opposite side of the diving goalkeeper.
Chelsea doubled their lead 15 minutes later with some great build-up play between Willian and Hazard, with the Brazilian receiving the ball back and stroking it past the on-rushing Ibrahim Sehic, giving the Blues a firm hold on the game.
Not content with the scoreline
Álvaro Morata had a glorious chance to put the match further out of the reach of Qarabag, however he squandered the opportunity by dragging his shot across the face of the goal and past the post.
However, the miss did not prove to be costly as the Azerbaijan champions had been lazy at the back with their passing, giving the ball away to Willian, who once again, was fouled in the penalty area.
Fàbregas stepped up and powered the ball past Sehic, who went the correct way on this occasion, however, could not get anywhere near the strike, scoring just his second goal of the season.
The Blues were not content with leaving the result at 3-0, having seen their first meeting ended at twice that scoreline, and Willian took it upon himself to make sure it did not finish that way.
The Brazilian took the ball forward from around 25 yards out and decided to unleash a powerful strike into the corner, leaving the goalkeeper absolutely no chance of stopping.
Eye on Saturday
Conte’s men will be pleased to have secured their place in the last 16 of the Champions League, however, the Italian will already turning his attention and focus to their trip to Anfield on Saturday against Liverpool.
Jürgen Klopp’s men had a mixed performance the night before, having squandered a 3-0 lead in Spain against Sevilla at half-time and finishing the game level, whilst Chelsea will need to travel back across Europe in order to prepare for the Premier League fixture.