Rotherham have not beaten Southend at home in seven attempts since 1980, and they never looked like breaking the hoodoo as the visitors leapfrogged above Rotherham at the top of the table following their 4-0 win.
Southend led from the 10th minute and really they deserved more for their first half showing than Peter Gilbert's strike.
Rotherham only cleared a right-wing corner to the edge of the penalty area and Gilbert fired home hard and low giving goalkeeper Conrad Logan no chance.
A minute earlier Logan had saved well from Michael Timlin and the visitors should have taken control after 16 minutes when a flowing move involving Liam Dickinson and Neil Harris ended with Timlin firing straight at Logan.
Rotherham didn't get into gear until just before the break when Alex Revell fired just wide after 35 minutes from Gareth Evans' cross.
And two minutes later Troy Brown's header from Danny Schofield's corner was blocked on the line by goalkeeper Glenn Morris and then hacked clear by Mark Phillips.
But two minutes after the restart, Southend doubled their lead. Rotherham again failed to defend a right wing corner and a half-hearted headed clearance was volleyed home by Timlin.
And on the hour, Timlin did it again. Rotherham again failed to deal with a right wing cross and Timlin ran on to the lose ball and smashed it past Logan.
And worse was to follow three minutes later. Again the cross came from the right, again Rotherham were all at sea and Neil Harris was left with a simple tap in.
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