The home side had produced a Herculean defensive performance to hold out against wave after wave of pressure in the closing 20 minutes.
But with Tony Pulis' men less than a minute away from an unlikely point, Maluda drove a 14-yard shot which took a deflection on its way past Steve Simonsen.
Pulis opted to challenge Chelsea's midfield trio man for man and the early stages were predictably tight with City's iron curtain - which included three central defenders - suffocating the visitors' attacking efforts.
But it was Stoke who posed the first real threat when a long ball by Ryan Shawcross led to a mistake from Branislav Ivanovic.
The big defender made a real mess of his attempt to shepherd the ball back to Petr Cech and James Beattie - with a clear sight of goal - snatched his shot wide from 20 yards.
It was the last taste of the action for Beattie, who appeared to suffer a recurrence of his recent knee injury and had to be stretchered from the field.
There were further question marks over Chelsea's defending - and this time goalkeeper Cech - when Stoke took a 32nd minute lead.
Cech started to come for Glenn Whelan's right-wing cross but was in no-man's land when Abdoulaye Faye planted a firm header beyond him and into the net.
Chelsea attempted to hit straight back as Ashley Cole fired at Thomas Sorensen, who limped off himself in the 41st minute after injuring his back as he made a clearance.
Lengthy delays caused by injuries to Beattie and Sorensen led to eight minutes of stoppage time and Stoke's second-choice keeper Simonsen was beaten in the third of them.
A wonderful reverse pass by Frank Lampard put in Didier Drogba, who spun past Faye before unleashing a fierce left-foot shot which ripped into the top left-hand corner of Simonsen's net.
Chelsea made a big effort to take hold of the game at the start of the second half, but Stoke held out with some authority and again started to pose a few problems of their own.
Dave Kitson and ex-Chelsea defender Robert Huth threatened with headers from corners by Whelan and Blues boss Carlo Ancelotti's response was to make a double substitution.
Nicolas Anelka and Michael Essien replaced Salamon Kalou and Michael Ballack and the changes stimulated an all-out assault.
Faye was immense at the heart of Stoke's defence and he had to be as Lampard, on three occasions, Drogba, twice, and Anelka were all denied before Malouda pounced.