The Spanish striker scored twice before Eden Hazard added an insurance goal in Gelsenkirchen.
The Spain striker, making his 100th start for Chelsea, opened the scoring with an early header and was on target again in the second half to take his tally to five goals in his past five Champions League games. And Eden Hazard put the icing on the cake with a third goal three minutes from time as Schalke pressed forward.
Jose Mourinho's side did not dominate in Gelsenkirchen on Tuesday, but the victory ensured Chelsea is now tied for the Group E lead along with its German opponents.
Schalke won their opening two matches in the group and had not conceded a goal before facing Chelsea, but a lack of cutting edge in the absence of the injured Klaas-Jan Huntelaar and Jefferson Farfan was evident.
Mourinho made five changes to the Chelsea side that beat Cardiff City in the Premier League on Saturday, with Cesar Azpilicueta starting in an unfamiliar left back role as Ryan Bertrand dropped to the bench.
Huntelaar (knee) and Farfan (groin) were sidelined for the hosts, but they did welcome back midfielders Kevin-Prince Boateng and Jermaine Jones along with goalkeeper Timo Hildebrand.
Torres was another player recalled to Chelsea's lineup, and he took less than two minutes to make his presence felt, turning sharply in the box and unleashing a shot that was deflected for a corner.
And the Spain striker opened the scoring three minutes later when Frank Lampard's corner was flicked on by Branislav Ivanovic and Torres found himself unmarked at the back post to head home.
Schalke started to find its stride. Marauding right back Atsuto Uchida burst into the Chelsea penalty area in the 26th minute, but blazed high and wide.
Boateng stung Petr Cech's palms with a long-range drive seven minutes before halftime, and from the resulting corner the Chelsea keeper had to be alert once again to tip over Roman Neustadter's towering header.
Torres was unfortunate not to double Chelsea's lead five minutes after the break when he met Lampard's inviting free kick with a glancing header that struck the bar.
The 29-year-old then got on the end of another Lampard corner but headed wide at the far post from close range before Cech palmed away a shot from Benedikt Howedes at the other end.
Howedes had another great chance but headed wide after 66 minutes, and he was made to pay when Chelsea extended its advantage three minutes later.
Schalke was caught in possession in midfield and Chelsea broke sharply, with Oscar racing down the right and finding Torres, who took a touch to round Hildebrand before slotting into the empty net.
And Hazard added a third three minutes from time when he raced through on goal and produced a clinical left-footed finish into the far corner.