The Spanish striker, with his new face mask in tow, opened the scoring for the Blues in the 16th minute when he used quick-thinking to prod the ball home whilst sitting on the ground after tussling with Rubin skipper Roman Sharonov.
The lead was doubled just after the half-hour mark when Victor Moses fired home the rebound from his initial header which had been kept out by Rubin keeper Sergei Ryzhikov.
Rubin found a way back into the contest when they were awarded a penalty after the ball struck the arm of captain John Terry with Bibras Natkho stepping up to the spot to send Petr Cech the wrong way.
The away goal could prove vital in the second leg as it gives Rubin some hope but that was slightly quashed when Chelsea scored a third with 20 minutes remaining.
Torres started a neat piece of play which involved Frank Lampard who played in Juan Mata to set up a cross for his fellow Spaniard to powerfully header home giving the Blues the advantage going into the return leg in Russia next Thursday.
2012/13 Europa League quarter-final – first leg