Torres converted from close range with nine minutes remaining – but television replays showed the Spaniard was clearly in an offside position when he turned home Ashley Cole's cross.
Visiting manager Brian McDermott was left incensed by the decision of referee Lee Mason to award the goal that undid his side's previous excellent work.
At that point Reading appeared to be on course to claim at least a point after goals from Pavel Pogrebnyak and Danny Guthrie – helped by an error by Chelsea keeper Petr Cech – had overturned Frank Lampard's early penalty.
Gary Cahill's long range shot had brought Chelsea level midway through the second half but the match was very much in the balance when Torres struck.
Then, in the very final seconds, Branislav Ivanovic capped a breakaway to roll in the fourth goal after Reading keeper Adam Federici had gone forward.
When the dust settled, European champions Chelsea could reflect on a second successive victory but there was little doubt they had benefited from a slice of good fortune and survived a major scare.
It was in stark contrast to the way they had marked the start of their league campaign with victory at Wigan.
And when the home side carried on where they had left off at the DW Stadium, the signs were ominous for Reading.
Eden Hazard, an immediate success in first Premier League game three days previously, again settled quickly collecting a second minute pass from Juan Mata before pulling his left foot shot narrowly wide.
Then the Belgian produced a moment of trickery to out-fox Reading right back Chris Gunter and win the 17th minute penalty that appeared to set Chelsea on course for a comfortable three points.
Lampard converted confidently from 12 yards and with Reading apparently unable to get near their sharper opponents it was hard to see a way back for the visitors.
The one bright spot for Reading during a torrid opening 25 minutes however, had been the sight of Pogrebnyak unsettling the Chelsea central defensive pair of Cahill – in for the injured David Luiz – and John Terry.
And the Russian equalised when Gareth McCleary picked him out in the 25th minute, escaping Cahill's marking and heading home from 12 yards out.
Reading were now instilled with a sense of belief and were further rewarded four minutes later after Jobi McAnuff's direct run towards the box was ended abruptly by a Terry foul.
Guthrie lined up the angled free kick from 25 yards out and was as surprised as anyone to see his low shot spill out of Cech's arms and over the line after the ball had been allowed to pass beneath the defensive wall.
Chelsea's shape had gone with the two holding midfielders – John Obi Mikel and Lampard – unable to protect the back four.
They were also unable to mesh with Mata, Hazard and Ramires, the three players operating in support of Torres.
The Spaniard, meanwhile, was having little impact on the game and missed a free header in first half added time.
Chelsea needed a slice of luck to get them back into the game and it came in the 69th minute when Cahill sent in a swerving shot from 30 yards.
The ball bounced in front of Federici but the keeper should have done better. – Sapa-AFP