Malouda drove home through a crowd of players with 23 minutes remaining to move the Premier League champions back into third place, two points clear of Manchester City.
But Torres' misery continued, the Spaniard flopping again in front of goal after coming off the bench for the final half-hour against a Wigan side who remained rooted to the foot of the table.
Torres' substitute role appears to indicate he will definitely start Tuesday night's Champions League quarter-final second leg at Manchester United.
Yet Wigan seemed tailor-made for the £50million man to end his now-infamous 12-hour goal drought, with Chelsea having scored 14 times in the sides' last two meetings.
The first of those saw Carlo Ancelotti clinch the Premier League title 11 months ago in a double-winning first season at Stamford Bridge.
It has all gone badly wrong since, with the Blues 11 points adrift of leaders United before kick-off here - and they put in a disjointed first 45 minutes at Stamford Bridge.
Abandoning their 4-4-2 formation in favour of a 4-3-3 appeared to have little effect, as they struggled to break down Latics.
As against United on Wednesday, Didier Drogba was their only real outlet and he created what should have been a first-minute opener when Frank Lampard and Ramires both mis-kicked his cross.
Drogba also laid on two chances for the recalled Malouda, who was thwarted by Ali Al Habsi.
With captain John Terry rested, the Blues defence also had its wobbles, with Charles N'Zogbia controversially flagged offside after being put clean through by Ben Watson and Hugo Rodallega causing consternation before Ashley Cole blocked his finish.
The visitors could still be forgiven a bit of time-wasting, which saw Emmerson Boyce booked, while David Luiz was lucky not to follow for clattering into Rodallega.
Ancelotti tried to freshen things up at half-time by sending on the fit-again Yossi Benayoun for his first appearance since September in place of Mikel.
Lampard drove narrowly wide from 20 yards after a sharp turn before Luiz tested referee Howard Webb's patience once too often by bundling into Rodallega and was booked.
Nicolas Anelka was withdrawn for Torres with just over half an hour remaining, much to the satisfaction of Chelsea owner Roman Abramovich.
But it was Drogba who almost made the breakthrough with a deflected free-kick tipped over by Al Habsi.
Wigan threw on Conor Sammon and Franco Di Santo for N'Zogbia and a non-plussed Rodallega, who stormed down the tunnel, before Torres sent a weak finish at Al Habsi after showing good skill to break into the box.
The deadlock was finally broken in the 67th minute when Torres prevented Al Habsi claiming Luiz's flick-on from Drogba's corner and Malouda drilled home through a crowd of players to claim his first goal in two and a half months.
Ramires was briefly forced from the field after taking a nasty kick to the knee from former Chelsea man Di Santo.
Torres went agonisingly close to getting on the end of Drogba's cross before failing to control a long ball which went straight through to Al Habsi.
Alex made his first appearance since November, coming on for Ferreira for the final 15 minutes.
Another miscontrol from Torres denied the striker a shot at goal before Wigan began to go for broke, Di Santo forcing a scrambling save from Petr Cech.
They also threw on Victor Moses for Diame but the final few minutes were all about Torres' increasingly-desperate attempts to find the net.
He looked certain to do so after Benayoun put the ball on a plate with a minute remaining but his strike was palmed behind by Al Habsi.
A stoppage-time Wigan surge saw Moses and Tom Cleverley thwarted and Maynor Figueroa booked for fouling Branislav Ivanovic, while Malouda had a second goal chalked off for an infringement.