Tes Bramble pounced in the 89th minute to give Southend all three points in a drab encounter at Roots Hall.
With the game heading for a goalless draw Barrington Belgrave was fouled by Simon Grand, but referee Iain Williamson played a crucial advantage.
Bramble raced on to the loose ball and rounded Dale keeper Neil Edwards before slotting the ball home into an unguarded net.
If there was to be a winner of this error-strewn encounter then it was the home side who were the more deserving, after they created the best of the chances.
Jay Smith tested Edwards inside 30 seconds and Mark Rawle saw a header cleared off the line by Wayne Evans.
Paul Connor and Bramble were also guilty of wasting first-half chances, and Rawle again went close with a long-range effort.
Dale's Lee McEvilly managed to put his long-range free-kick out for a throw in and that just about summed up their first half, until Clive Platt headed wide in the closing seconds of the period.
The second half saw little in the way of goalmouth action although Rochdale player-manager Paul Simpson forced the Shrimpers Danny Gay into an acrobatic save.
Daniel Marney and Leon Cort failed to threaten the visitor's goal when presented with good opportunities and a goalless stalemate looked certain until Bramble's dramatic late intervention.