Torres appeared a yard in front of play when he completed his side's comeback from 2-1 down in an early-season thriller but his finish was allowed to stand by Lee Mason and his assistants.
It was harsh on Reading, who brilliantly battled back from Frank Lampard's penalty to lead at half-time through Pavel Pogrebnyak and Danny Guthrie.
Guthrie's goal came courtesy of a Petr Cech howler and opposite number Adam Federici had a nightmare of his own - his second in five days - in conceding Gary Cahill's equaliser.
Branislav Ivanovic scored into an empty net in the final minute of stoppage-time after Federici bombed forward in search of a draw.
The victory put Chelsea top of the table for the first time since November 2010, a fact pointed out by manager Roberto Di Matteo ahead of a fixture brought forward due to the European champions' involvement in the UEFA Super Cup.
But the Italian will be concerned at how hard his side made it for themselves against the npower Championship winners, who had several other chances to score.
For 25 minutes, it was the Chelsea show, with Eden Hazard showing the skills that yesterday saw Di Matteo dub him an "artist".
The Belgian had taken less than two minutes to make his mark on his league debut at Wigan and it could have been the same story tonight had he not screwed Juan Mata's through ball wide.
Hazard, Mata and Ramires were constantly on the move behind Torres and more fine football saw the latter force a good stop from Federici.
Torres went close to a superb solo goal before Chelsea inevitably took the lead in the 18th minute, the skills of Hazard again the inspiration.
The £32million man tormented Chris Gunter to distraction and when the leg was dangled, he hit the deck, giving Mason no choice but to award the penalty, Lampard giving Federici no chance from the spot.
If Chelsea thought the floodgates would open, they were given the rudest possible awakening as Reading amazingly turned the game on its head in the space of four minutes.
Pogrebnyak equalised with a brilliant header, getting in front of Cahill to glance home Garath McCleary's cross.
But the visitors had an almighty howler from Cech to thank for going in front, the goalkeeper embarrassingly allowing Guthrie's powerful free-kick to spin off his body and into the net.
John Terry powered over a header from Mata's free-kick and Hazard's blockbuster was also too high but Chelsea had lost the initiative and had lost their way at the back.
Terry was being given a torrid time on his 550th club appearance and conceded a free-kick that Ian Harte whipped in and Alex Pearce somehow failed to connect with.
Torres could also have done better than glance wide a pinpoint Hazard cross on the stroke of half-time.
Ivanovic blazed over after the restart but Chelsea were struggling to penetrate a wall of yellow as Di Matteo sent on Oscar for Ramires before the hour mark.
Jem Karacan became the first player booked for upending Mata and Pogrebnyak quickly followed for tripping Ashley Cole but the home side were just as ragged.
They were rushing what few shots they had, Hazard's blocked effort typical of their floundering, and Di Matteo took action again when he threw on Daniel Sturridge for John Obi Mikel in the 68th minute.
It immediately paid off in unexpected fashion thanks to another goalkeeping howler from Federici, who palmed Cahill's swerving 25-yarder into his own net.
Reading sent on Adam Le Fondre for Karacan and Noel Hunt for Pogrebnyak but the force was with Chelsea and Mata screwed wide before they completed their own comeback thanks to a huge slice of luck.
The build-up was the equal of anything they had produced all evening but Torres appeared clearly offside tapping home Cole's low cross.
Reading went for broke late on, with Hal Robson-Kanu replacing McCleary and Federici bombing forward and they were caught out when Hazard squared for Ivanovic to tap home.