He smashed the ball into the corner after it had been laid back to him by substitute Nicolas Anelka.
It was tough luck on Stoke, who had gone ahead through Abdoulaye Faye only for Didier Drogba to equalise in first-half stoppage time.
James Beattie should have put Stoke ahead in the ninth minute but scuffed a shot wide. In the process he suffered a recurrence of his ankle injury and was stretchered off to be replaced by Ricardo Fuller in the 11th minute.
Stoke made the breakthrough in the 32nd minute after Glenn Whelan swung in a cross. Skipper Faye reacted first and powered a header beyond Petr Cech.
Stoke lost their second player of the half with Thomas Sorensen coming off injured in the 41st minute and was replaced by Steve Simonsen.
In first-half stoppage time Drogba pulled Chelsea level with a shot into the corner following a superb through ball from Frank Lampard.
Chelsea stepped up the pace in the second half and Drogba thumped in a shot after 76 minutes but Faye made a brave block.
Drogba then whipped in a free-kick from 25 yards, only for Simonsen save well.
Stoke appeared to be holding out only for Malouda to have the last word.