First-half goals from Dudley Campbell and Stephen Clemence, plus second-half strikes from Gary McSheffrey and Radhi Jaidi made it ten wins in 12 matches for Blues in their bid to bounce straight back to the top-flight.
Blues took the lead after seven minutes when McSheffrey's cross found Campbell 16 yards out at the far post and he slammed the ball past Darryl Flahavan.
But home fans immediately started chants of "1-0 to the referee" after Shrimpers striker Lee Bradbury was brought down by a two-footed Jaidi challenge in the build-up to the goal.
The Blues central defender was involved in the action again minutes later when his timely challenge halted Alan McCormack's goalward charge as Southend pressed for an equaliser.
Mark Gower then lofted the ball to McCormack in the 34th minute, but he fired into the side-netting when it seemed easier to score.
That miss increased in importance three minutes later when Nicklas Bendtner's cross into the box was only partially cleared by Efe Sodje, and Clemence was on hand to beat Flahavan at his far post.
Southend saw Freddy Eastwood head narrowly over from Mark Hammell's free-kick, but it was Blues who looked in control.
Blues maintained the pressure with Jaidi just off target, while Campbell had the ball in the net but referee Mike Thorpe had blown for a foul on the edge of the box.
The travelling fans were furious the advantage had not been played, but it was irrelevant as McSheffrey curled the free-kick round the wall and into the net.
Gary Hooper wasted a great chance to reduce the arrears when he shot wide from Gower's header.
Blues keeper Maik Taylor then saved Steve Hammell's free-kick before the leaders wrapped things up when Jaidi headed home Johnson's right-wing cross from six yards at the far post six minutes from time.