Rafa Benitez opted to rotate the squad, with the club playing their third match in the space of six days. Yossi Benayoun was handed a rare start, while Ryan Bertrand and Moses were also given the opportunity to impress.
The Blues were on top for the majority of the game, but at times the Russians showed exactly what they can do, with Gokhan Karadeniz and Natcho both menaces throughout.
And with the return leg just one week away, there was much to take away from the game and reflect upon.
Was it just a one-off from Torres?
Is 3-1 a big enough margin?
Find out the answers right here, as we look at six things to take from the game at Stamford Bridge.
He may be having a torrid time scoring in the Premier League, but Fernando Torres' brace against Rubin Kazan highlighted a superb turnaround in fortunes for the Spaniard.
His first goal may not have been a touch of class, but his movement to latch onto David Luiz's excellent lofted pass was somewhat reminiscent of the "Torres of old" many commentators tend to invoke.
He sprung half a yard away from the Rubin defender, and after controlling the ball—albeit with a slice of luck—he bundled the ball home with a gentle prod.
The goal immediately gave him a boost in confidence; Torres even went as far as trying an audacious rabona—a skill only attempted now and then on the football pitch. But he executed it with brilliant technique and found a teammate in the area.
His second goal, however, was even more impressive. Juan Mata ran out to the right and swung in a stunning cross which was met by a powerful header from Torres into the top corner.
Again, the movement was timed to perfection, and it displayed the kind of form which convinced Roman Abramovich to pay £50 million for the former Liverpool man. That was his sixth goal in 12 European appearances this season—and even more impressive, it was his third in his last two Europa League games.
Even if Demba Ba was available, there's no doubt who would be Chelsea's main man in Europe.
Benayoun, Moses and Torres have been on the fringes this season
Rafa Benitez has always been an admirer of squad rotation, and for many years, his decision to consistently tinker with the team selection has been met with disapproval.
But it seems that with Chelsea already playing over 60 games this season—which could reach 70 if they reach the finals of both the Europa League and FA Cup—squad rotation is not a choice; rather, it's a necessity.
Despite complaining about the lack of numbers in his squad, Benitez has used three different teams in the space of six days against Southampton, Manchester United and now Rubin Kazan. The club has won two out of those three matches, and one can't help but accept that his tactics have worked a treat.
After the 3-1 victory, the Blues have one foot in the semi-finals of the Europa League, although a long trip back to the haunting Luzhniki Stadium in Moscow awaits the West London club.
Benitez will no doubt put out a weakened side with the aim of protecting their two-goal margin.
So far, rotating the squad has worked to their advantage; let's hope for Benitez's sake it turns out well for him once again.
There will be many who will judge Jose Salomon Rondon's performance against Chelsea tonight as below-par.
And it was—there is no doubt about that.
Mustering just one feeble attempt on goal, his movement was dangerous at times, but he never really got into the game after coming on after 46 minutes.
The Venezuelan striker, who moved to Rubin in the summer for a reported fee of around £8.5 million from cash-strapped Malaga, has endured a difficult start to his career in Russia, scoring six goals in the process. Four of them have come in the Europa League.
He, along with other Rubin players such as former Blues midfielder Gokhan Tore, may be baffled as to why they started on the bench when their combined value totals up to £17 million. Surely, two big-name players need to start a game of this magnitude.
The 24-year-old will be desperate to put himself in the shop window in the return leg in a week's time, although it would appear that from the way Chelsea dealt with the forward in Thursday's game, Rubin may adopt a similar approach in Moscow.
Surely there are no doubters about Juan Mata's ability, especially after putting in yet another spectacular showing at Stamford Bridge.
Setting up his compatriot Fernando Torres with a cross straight out of heaven, Mata now has an incredible record of 18 goals and 32 assists in 52 appearances this season for Chelsea.
That is on average just under a goal or assist a game for Mata this campaign. Quite incredible.
And to think, Mata is just 24 years of age. To face him in current form is worrying enough for defenders, but to think he could still get better is frightening.
Yet, while he is without doubt the first name on the team sheet for his club nowadays, the Player of the Year does not feature regularly enough for his country, despite scoring in the Euro 2012 Final.
Vicente Del Bosque continues to select Cesc Fabregas in front of Mata, despite the former Arsenal man struggling for form at current club Barcelona. Why? Your guess is as good as mine.
One thing is for certain, though: It will be impossible for Del Bosque to resist picking the little magician if he can continue in this rich vein of form.
Natcho's penalty may be viewed as simply just a consolation in this 3-1 defeat to Chelsea, but Rubin Kazan coach Kurban Berdyev will view it as a lifeline for this tie.
Chelsea may argue until they are blue in the face—pun not intended—that it should not have been a penalty. But in any case, it was a cool finish from Natcho.
An away goal is always vital, especially when your home ground is based in a hostile Moscow atmosphere. To go through, Rubin need to win 2-0 in Moscow, or if Chelsea score, by three clear goals. Nevertheless, Berdyev will be confident that his side can get the two goals they require.
The Russian has been in charge of the club for an impressive spell extending to 12 years, which highlights a sense of stability, especially so when you compare them to their not-so-loyal English counterparts.
In Chelsea's view, they have one foot in the semi-final. Rubin, however, will feel there is still much to play for.
Although most eyes will be on Fernando Torres' surprise brace in Chelsea's 3-1 victory over Rubin Kazan, one must also consider the effect of their ever-changing defensive partnership.
Many different combinations have been tried this season without effectively establishing the most efficient pairing. John Terry, David Luiz, Branislav Ivanovic, Gary Cahill and even Paulo Ferreira have played at center-half for Chelsea in the last year or so, but without any conclusive results.
However, you get the feeling that Rafa Benitez is edging towards the pairing of Terry and Luiz as his favored partnership after Thursday's performance.
Terry showed that he still possesses quality and leadership on the field, despite a dubious handball for which he was penalized. His positioning is crucial, as at 32 years of age, he lacks the extra yard in pace he used to have.
As for Luiz, in many ways he is a younger version of Terry in terms of leadership. His positioning needs work, as seen tonight when he allowed Jose Rondon to skip past him, but his assist for Torres' opener exhibits the need to have him in the side.
A combination of his pace with Terry's reading of the game is effective, and for Chelsea, it's a pairing that could define the next few years in defense.