Fernando Torres scored his 17th and 18th goals of the season with Victor Moses netting his seventh to give the Blues a lead to take to Russia next week.
The Spaniard opened the scoring, scrambling the ball in from close range and headed in the third goal in the second half after a good move. Moses had made it 2-0 in the opening period with the goal of the night but Rubin Kazan pulled one back from the penalty spot before the interval. For most of the game though, it had been a solid Chelsea defence with the Blues on top across the park.
There were six changes to the side that began the win over Man United with John Terry and Ryan Bertrand coming into defence, Frank Lampard back in midfield and Fernando Torres in attack with Demba Ba cup-tied.
Yossi Benayoun began wide of Juan Mata with Victor Moses another player returning to the starting line-up on the other flank. David Luiz played the 50th European game of his career.
Rubin Kazan changed their shape from their last-round win over Levante, from 4-2-3-1 to 4-4-1-1 -Roman Eremenko supporting centre-forward Vladmir Dyadyun.
The message had been clear before the game, Chelsea wanted goals and a good lead to take into a never-easy second leg in Moscow.
Benayoun, in his start since the first leg away in Bucharest last round, was the first to show enterprise but his dribble into the box came to a halt before any end product.
Mata showed similar good control on 10 minutes to get through a crowd inside the area but when he squared, a flick off a Rubin shin diverted the ball from danger. Torres turned his marker soon after as he chested a Lampard pass from halfway but bobbled a shot wide.
The quick long pass up front appeared to be a clear tactic tonight, testing the Rubin central defence regularly, and 15 minutes Torres made them pay.
David Luiz sent the missile forward and although Torres's initial control left him, the ball and the defender together on the floor, it was the Spaniard who reacted quicker to stab the ball home from just a couple of yards out.
Chelsea v Rubin
Cech made his first save, from a speculative strike from Natcho, before Chelsea attacked again and this time it was Bertrand who from his own half snaked his way through. It was a thrilling run but the left-back's angled shot was cleared inside the six-yard area.
The game was steadily becoming one of constant Chelsea pressure and it was a sustained attack just past the half-hour mark that led to Moses doubling the lead.
The Russians had more than one chance to clear properly but they failed to do so. Azpilicueta 's cross led to a blocked Torres shot that spun up to Moses. His bouncing header was clawed wide by the keeper but a Torres cross was deflected back into Moses's path on the edge if the area. He fired into the top corner in style.
Chelsea v Rubin
Rubin pulled a goal back five minutes before half-time and given the balance of the game at that stage, from possibly the only route available to them. Ansaldi fired the ball in the direction of the goal and it hit the arm of Terry which was pretty much down by his side. That was enough for the referee to point to the spot and book our skipper. Natcho converted the penalty.
The 30 or so Rubin Kazan fans present were very pleased with that away strike, as they would have been with the single-goal deficit at half-time given Chelsea's superiority.
Rubin Kazan swapped centre-forwards for the restart - the tall Venezuelan Jose Rondon replacing Dyadyun.
With four minutes of the half gone, it needed a full-stretch save from the keeper to keep out Moses's shot, a quick switch of play having created space. Moses touched the ball into the Chelsea topscorer's path after a David Luiz cross. The ball ran loose after the save but it was cleared before Terry could snap it up.
There was a rare moment when Cech went for but didn't claim a corner which served to emphasise the need for more goals.
Just before the hour Torres hit a good cross to the far post which won a corner. Mata was not far from serving that up perfectly for Terry but the header cleared the bar.
The next chance worryingly was Rubin's and had Rondon not hit it straight at Cech then we would have been in trouble. Benitez brought on Hazard for Moses soon after.
The reassuring third goal came from a swift counter-attack down the left. Benayoun released Torres and although the striker was initially held up by a group of defenders, he involved Lampard in the move who in turn found Mata peeling away to the flank. The cross was floated in and Torres made no mistake with his head. There were 69 minutes played.
Chelsea v Rubin
Benayoun was booked for sliding in on Ansaldi moments before the second Chelsea substitution. It was time for Mata to rest, Oscar coming on. Marin then followed for Benayoun who came off to good applause. It had been his third start of the season.
The final shot was a long-range dig from Ramires which was a worthy effort, the Brazilian having just been fouled to earn Orbiaz a booking. Marin also received a late yellow card.
Chelsea (4-2-3-1): Cech; Azpilicueta, David Luiz, Terry (c), Bertrand; Ramires, Lampard; Moses (Hazard 65), Mata (Oscar 77), Benayoun (Marin 82); Torres.
Unused subs Turnbull, Ferreira, Ivanovic, Mikel.
Scorers Torres 16, 69, Moses 32.
Booked Terry 40, Benayoun 77, Marin 90+2.
Rubin Kazan (4-4-1-1): Ryzhikov; Kaleshin, Sharonov (c), Navas, Ansaldi; Kuzmin (Kasaev 82), Orbaiz, Natcho, Karadeniz; Eremenko; Dyadyun (Rondón h-t).
Unused subs: Arlauskis, Marcano, Ryazantsev, Kislyak, Tore.
Scorer Natcho 41 pen.
Booked Orbaiz 86
Referee Gianluca Rocchi from Italy.