Chelsea are bidding to become only the fourth side to win all three of Uefa's major club competitions. The Blues, who won the European Cup Winners' Cup in 1971 and 1998, plus last season's Champions League, would emulate Juventus, Ajax and Bayern Munich.
But they survived any further damage after Natcho's spot-kick made it 3-2 to the home side.
It means the much-maligned Benitez remains on course to win two trophies for the west London club and finish in the top four of the Premier League.
Chelsea's dominant display at Stamford Bridge a week earlier left Rubin with a difficult task, which was made even harder following Torres's early opener.
Frank Lampard showed remarkable vision to send Torres clear with a clinical first-time pass and when Rubin goalkeeper Sergei Ryzhikov raced out of his goal, the Spaniard coolly lobbed the ball into the empty net for his 19th goal of the season.
It left Rubin needing three goals to force extra-time but the complexion of the tie could have been different, had Rubin not spurned a glorious opportunity seconds earlier.
The Russians should have taken the lead when skipper Karadeniz picked out Roman Eremenko in space inside the visitors' penalty area, only for the Finland international to fire straight at Chelsea skipper John Terry.
Veteran Portuguese defender Paulo Ferreira made only his sixth appearance of the season in Moscow. All six matches have been in different competitions.
Uefa ruled the match should be played in the Russian capital after concerns about Kazan's Central Stadium, and only 19,000 spectators were present in the 80,000-capacity ground.
Rubin boss Kurban Berdyev argued the switch had damaged his side's chances of progressing but, after the early blow of Torres's goal, the Russians gave themselves a lifeline shortly after the second-half restart.
Pablo Orbaiz's in-swinging cross from the right was powerfully met by Spanish compatriot Marcano, whose accurate header flew into Petr Cech's top corner.
The Russians were left deflated again when Moses stylishly steered past Ryzhikov following a neat exchange of passes with Ramires.
But they refused to give up as Karadeniz climbed above Dutch teenager Nathan Ake, making only his second professional start for Chelsea, to bury Cristian Ansaldi's cross from the left touchline.
Marcano again found space inside the Blues' six-yard box, only to flash a header wide, before Natcho blasted past Cech after substitute Aleksandr Ryazantsev fell under Cesar Azpilicueta's innocuous challenge.
Chelsea saw out the final 15 minutes to reach their 18th semi-final appearance of the Roman Abramovich era, where they will face either Benfica, Fenerbahce or Basel.
Emboaba Oscar takes a shot. Save made by Sergei Ryzhikov.
Foul by Paulo Ferreira on Gokdeniz Karadeniz, free kick awarded. Free kick crossed right-footed by Bebras Natcho, clearance by Paulo Ferreira.
90:00 +0:31 Substitution
Substitution Branislav Ivanovic comes on in place of Frank Lampard.
Bebras Natcho restarts play with the free kick.
90:00 +0:15 Booking
Booking Caution for Emboaba Oscar.
Emboaba Oscar concedes a free kick for a foul on Gokdeniz Karadeniz.
Ivan Marcano takes a shot. Save by Petr Cech.
Inswinging corner taken from the right by-line by Bebras Natcho.
A cross is delivered by Vitali Kaleshin, clearance made by Cesar Azpilicueta.
Gokdeniz Karadeniz gives away a free kick for an unfair challenge on Paulo Ferreira. Paulo Ferreira takes the free kick.
Paulo Ferreira takes the free kick.
Booking Ivan Marcano is shown a yellow card.
Unfair challenge on Fernando Torres by Ivan Marcano results in a free kick.
Emboaba Oscar takes a short corner.
Effort from the edge of the area by Roman Eremenko goes wide of the right-hand upright.
Corner taken by Emboaba Oscar, clearance made by Cristian Ansaldi.
Jose Salomon Rondon takes a shot. Petr Cech makes a save.
A cross is delivered by Gokdeniz Karadeniz, clearance made by John Terry.
Vladimir Dyadyun produces a right-footed shot from just outside the penalty box that misses to the left of the target.
Substitution Emboaba Oscar joins the action as a substitute, replacing Yossi Benayoun.
Victor Moses takes a shot from just outside the penalty area clears the crossbar.
74:26 Goal scored
Goal! - Bebras Natcho - R Kazan 3 - 2 Chelsea Placed penalty scored by Bebras Natcho. Rubin Kazan 3 (4)-(5) 2 Chelsea.
Alexander Ryazantsev fouled by Cesar Azpilicueta, the ref awards a Penalty.
Substitution (Rubin Kazan) makes a substitution, with Alexander Ryazantsev coming on for Alan Kasaev.
The ball is swung over by Gokdeniz Karadeniz, clearance by Cesar Azpilicueta.
Free kick awarded for a foul by Alan Kasaev on John Terry. Direct free kick taken by Petr Cech.
Substitution Vladimir Dyadyun joins the action as a substitute, replacing Pablo Orbaiz.
Headed effort on goal by Ivan Marcano from inside the penalty box misses to the right of the goal.
Mikel concedes a free kick for a foul on Bebras Natcho. Free kick taken by Pablo Orbaiz.
Mikel challenges Roman Eremenko unfairly and gives away a free kick. Pablo Orbaiz restarts play with the free kick.
Cristian Ansaldi provided the assist for the goal.
61:37 Goal scored
Goal! - Gokdeniz Karadeniz - R Kazan 2 - 2 Chelsea Gokdeniz Karadeniz finds the net with a headed goal from close in. Rubin Kazan 2 (3)-(5) 2 Chelsea.
A cross is delivered by Bebras Natcho, Cesar Azpilicueta gets a block in.
Substitution Mikel is brought on as a substitute for Nascimento Ramires.
Nascimento Ramires has shot on goal from just outside the area which goes wide of the right-hand upright.
Roman Eremenko takes a shot. Alan Kasaev gets a block in.
The assist for the goal came from Nascimento Ramires.
54:57 Goal scored
Goal! - Victor Moses - R Kazan 1 - 2 Chelsea Goal scored by Victor Moses from inside the penalty area to the top right corner of the goal. Rubin Kazan 1 (2)-(5) 2 Chelsea.
Foul by Fernando Torres on Cristian Ansaldi, free kick awarded. Pablo Orbaiz takes the free kick.
The ball is sent over by Cristian Ansaldi, David Luiz manages to make a clearance.
Assist on the goal came from Pablo Orbaiz.
50:21 Goal scored
Goal! - Ivan Marcano - R Kazan 1 - 1 Chelsea Ivan Marcano finds the back of the net with a headed goal from inside the penalty area. Rubin Kazan 1 (2)-(4) 1 Chelsea.
Gokdeniz Karadeniz decides to take the corner short.
Yossi Benayoun fouled by Alan Kasaev, the ref awards a free kick. Direct free kick taken by Petr Cech.
The game restarts for the second half.
45:00 +1:50 Half time
Half Time The first half comes to an end.
Corner taken short by Gokdeniz Karadeniz.
Gokdeniz Karadeniz takes a shot. Petr Cech makes a save.
Substitution Oleg Kuzmin leaves the field to be replaced by Vitali Kaleshin.
Alan Kasaev fouled by Cesar Azpilicueta, the ref awards a free kick. Direct free kick taken by Gonzalez Cesar Navas.
The ball is sent over by Frank Lampard, save by Sergei Ryzhikov.
Cristian Ansaldi is caught offside. Direct free kick taken by Petr Cech.
Bebras Natcho takes a shot. Save by Petr Cech.
The ball is swung over by Cristian Ansaldi.
Roman Eremenko takes a shot. Petr Cech makes a save.
Roman Eremenko crosses the ball, Petr Cech makes a comfortable save.
Victor Moses sends in a cross, Ivan Marcano manages to make a clearance.
Shot by Jose Salomon Rondon from deep inside the penalty area misses to the right of the goal.
Pablo Orbaiz is penalised for a handball. David Luiz restarts play with the free kick.
The ball is crossed by Victor Moses, Frank Lampard takes a shot. Save made by Sergei Ryzhikov.
Alan Kasaev sends in a cross.
Roman Eremenko takes a shot. Comfortable save by Petr Cech.
Shot from just outside the penalty box by Jose Salomon Rondon misses to the left of the target.
Gokdeniz Karadeniz concedes a free kick for a foul on Victor Moses. Free kick taken by Paulo Ferreira.
Victor Moses takes a shot. Sergei Ryzhikov makes a save.
Foul by Ivan Marcano on Fernando Torres, free kick awarded. Free kick taken by Frank Lampard.
Pablo Orbaiz gives away a free kick for an unfair challenge on Victor Moses. Free kick crossed by Frank Lampard, Foul by David Luiz on Gonzalez Cesar Navas, free kick awarded. Sergei Ryzhikov takes the direct free kick.
The ball is swung over by Fernando Torres.
Pablo Orbaiz produces a cross, clearance by Nathan Ake.
The ball is crossed by Cristian Ansaldi, Yossi Benayoun gets a block in.
Effort on goal by Roman Eremenko from outside the box goes harmlessly over the bar.
Assist on the goal came from Frank Lampard.
4:02 Goal scored
Goal! - Fernando Torres - R Kazan 0 - 1 Chelsea A goal is scored by Fernando Torres from outside the penalty area to the top right corner of the goal. Rubin Kazan 0 (1)-(4) 1 Chelsea.
Roman Eremenko takes a shot. Blocked by John Terry.
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