The striker netted a scrappy opener after 16 minutes before Victor Moses doubled the advantage in the 33rd minute.
Bebras Natcho pulled a goal back for Rubin before the interval, converting a penalty after John Terry was adjudged to have blocked a shot with his arm, but Torres struck again after 70 minutes to put the Blues in the driving seat.
Benfica will also take a 3-1 lead into the return leg of its tie with Newcastle United.
Although the Portuguese host trailed to a goal from Papiss Cisse after 12 minutes, Rodrigo levelled matters 13 minutes later before second-half goals from Rodrigo Lima (65) and Oscar Cardoza (71), the latter from the penalty spot, secured the win in Lisbon.
Fenerbahce took advantage of the 49th-minute dismissal of Ogenyi Onazi to beat 10-man Lazio 2-0.
The Turkish host left it late, though, with Pierre Webo opening the scoring from the spot after 79 minutes before Dirk Kuyt added another in the dying seconds.
Tottenham Hotspur came from two goals down to play out a 2-2 draw with Basel at White Hart Lane.
Two goals in five minutes from Valentin Stocker (30) and Fabian Frei (35) gave the Swiss visitor two welcome away goals.
However, Tottenham gave itself a fighting chance ahead of next week's return leg with replies from Emmanuel Adebayor (40) and Gylfi Sigurdsson (58).