Southend had a let-off in the 14th minute when Burton's on-loan Aston Villa striker James Collins fired wide from the spot after being tripped by Graham Coughlan.
Collins was shown the way to goal as team-mate Jacques Maghoma broke the deadlock by turning home Russell Penn's cross from six yards in the 37th minute.
And Southend were in deeper trouble in added time at the end of the first half when a Scott Malone free kick glanced off the head of Luke Prosser and into his own net.
A double substitution by the visitors quickly paid dividends when Blair Sturrock headed home Ryan Hall's free kick in the 50th minute.
But it took Burton only six minutes to restore their two-goal lead with a superb 20-yard shot by Webster and only a fine save by Glenn Morris to deny Shaun Harrad spared Southend a heavier defeat.
Source: PA
Source: PA