Goals from Shaun Goater and Freddy Eastwood saw the Shrimpers depose bitter Essex rivals Colchester United from top spot and extend relegation-haunted Rotherham's winless run to seven matches.
Millers chairman Peter Ruchniewicz has warned the club could fold within weeks if they fail to stem a £140,000-a-month loss and the Yorkshire club has launched a Save Our Millers appeal.
Rotherham's defence cut out much of the early Southend danger but the Millers found themselves a goal down after 12 minutes.
Eastwood picked the ball up in midfield and picked out Mark Gower on the left. His shot cannoned off the right upright with goalkeeper Gary Montgomery beaten, but Goater raced in to score from close range.
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Southend countered with efforts from Eastwood and Mark Bentley but they were safely dealt with by Montgomery.
The visiting goalkeeper was picking the ball out of the net again after 36 minutes when Eastwood scored from an acute angle following a neat one-two with strike partner Goater.
The Millers refused to let their heads drop and could have reduced the arrears before the half-time whistle when Jonathan Forte and Lee Williamson both forced close-range saves from Flahavan.
The home shot-stopper again denied Rotherham a route back into the game six minutes after the restart when he twice saved from Shaw after the striker
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And it was Rotherham who continued to look the better side as the half progressed and they pinned the hosts in their own half for long periods.
Mullin tried a looping shot on the hour that was collected by Flahavan, but the visitors failed to find the final ball.
With a two-goal cushion Southend were happy to soak up the pressure and attack on the break.
Their best chance of extending their lead came on 77 minutes when substitute striker Lee Bradbury made a good run but saw his shot saved by Montgomery.
Rotherham's poor luck in front of goal was summed up a minute from time when Quinn's 25-yard free-kick curled over the wall but was saved by the diving Flahavan.