The centre-back sent a powerful header across the path of a despairing Carlo Cudicini to send the 6,000 away fans into raptures just as the referee was about to blow the final whistle.
Multimillionaires Chelsea had only themselves to blame as their total dominance of possession and chances resulted in just one goal - a header by Salomon Kalou.
Chelsea almost stole it back with the final kick of the game but goalkeeper Steve Mildenhall brilliantly dived to stop a Franco di Santo downward header.
Chelsea started the game as befitting a side in the top-flight and Didier Drogba was denied in the 10th minute by a last-ditch tackle by Osei Sankofa as the Ivory Coast striker was about to slot the ball home from eight yards out.
Joe Cole then flashed a low left-footer across Mildenhall's goal after a fine pass by Frank Lampard two minutes later.
Ashley Cole should have put the home side ahead on 22nd minute when he cut into the Southend penalty area. He unleashed a fine right-footer which Mildenhall parried away expertly.
Drogba and Joe Cole conspired to mess up another chance as Chelsea attacked at will.
But the breakthrough came on 31 minutes when a Lampard corner was met perfectly by the head of an unmarked Kalou at the far post and he aimed the ball accurately into the net.
The second half started much like the first with Chelsea on the front foot and a Drogba header from a Juliano Belletti cross forcing a save from Mildenhall on 53 minutes.
Constant raids by Chelsea with shots from Kalou, Belletti and Lampard all came to nothing.
Belletti almost scored with a powerful header on 67 minutes but the ball was cleared off the line by Johnny Herd.
Ashley Cole became the umpteenth Chelsea player to miss when he skied over the Southend goal on with 19 minutes remaining.
Southend boss Steve Tilson decided on a triple substitution on 74 minutes by bringing on Dougie Freedman for Lee Barnard, Franck Moussa for Jean-Francois Christophe and Francis Laurent for Alex Revell in an attempt to change the course of the game in their favour.
Southend almost nabbed an unlikely equaliser six minutes from time when Clarke headed the ball onto the Chelsea crossbar - before he rose majestically to grab the goal and all the headlines.