Torres, who scored twice in the 3-1 first-leg win, struck his 19th of the season after four minutes, but thereafter Chelsea endured a difficult evening on the synthetic surface.
Three goals in 13 second-half minutes, two of them for Rubin, had Chelsea worried, as Ivan Marcano and Gokdeniz Karadeniz scored headers either side of Victor Moses' curled effort. Bebras Natcho's 75th-minute penalty led to an anxious conclusion, but Chelsea held on to advance to the semi-final draw 5-4 on aggregate.
Nathan Ake made his second senior start as one of seven changes from the Sunderland win, while Paulo Ferreira, who required treatment in the opening skirmishes, featured at left-back due to the absences of Ashley Cole (hamstring) and Ryan Bertrand (illness).
It was Frank Lampard's first-time lofted through ball which sent Torres clear with the Blues' first attack and the Spaniard showed the finishing instinct which has so often been lacking during his spell at Stamford Bridge since his £50million transfer from Liverpool. His first touch saw him lift the ball over the advancing goalkeeper Sergei Ryzhikov for it to bounce once and go into the net.
Chelsea were prepared to sit and play on the counter-attack, with Ake and Ramires effective at breaking up play as Rubin went forward. On the few occasions when the defence was breached, Rubin failed to trouble Petr Cech in goal.
But Rubin equalised six minutes into the second half when Pablo Orbaiz's cross was met by Marcano, who rose above Ramires to direct a powerful header into the net.
Fortunately for Chelsea their response was almost immediate. Ramires won the ball from Orbaiz and laid it off to Lampard, who found Moses. The Nigeria international played a one-two with Ramires and curled a shot into the top corner.
But Rubin hit back quickly, as Cristian Ansaldi took Cesar Azpilicueta to the byline and crossed for the late-running Karadeniz, the smallest player on the pitch, to power a header beyond Cech.
Azpilicueta fouled Aleksandr Ryazantsev to grant Rubin a second penalty of the tie, which, like at Stamford Bridge, Natcho converted. Time and again Chelsea had to repel Rubin attacks in the closing moments and reinforcements were called as Branislav Ivanovic was brought on for stoppage time as the Blues advanced.
Source: PA
Source: PA