They were second best all the way through and Southend thoroughly deserved their passage into the fourth round of the Carling Cup.
The new Leeds boss watched from a box in the East Stand and can't have been very impressed by what he saw, especially from the Leeds defence.
Having conceded 11 goals in their last three outings, Leeds produced two more schoolboy errors in the first half to give Southend a 2-0 lead.
First Stephen Crainey chased after Simon Francis and pulled him down in the area to earn a yellow card. Steve Hammell dispatched the penalty low to Tony Warner's right.
A minute later, Matthew Kilgallon, back from a one-match suspension, dawdled over a clearance and then hit it weakly straight to Gary Hooper who hammered it into the net.
It was no more than Southend deserved. They had been the better side and put Leeds under plenty of pressure.
Only a stunning save from Warner had stopped them leading earlier as the recalled keeper somehow palmed away a powerful header from Efe Sodje.
Stung by the two goals, Leeds started to mount some kind of comeback and pulled a goal back a minute before the break when Ian Moore forced the ball home after efforts from Frazer Richardson and David Healy had been blocked.
Leeds tried to up the pace in the second half but were still giving the ball away too much and failed to test Darryl Flahaven.
Southend were much brighter and only excellent sweeping by Warner stopped Hooper after the striker had skinned Paul Butler, but even the Leeds keeper couldn't prevent Hooper scoring in the 64th minute.
Kilgallon managed to block Luke Guttridge's effort from Francis' cross but Hooper was on hand to hook in his second.
Stand-in manager David Geddis sent on Richard Cresswell and gave a debut to teenager Robert Bayly with 20 minutes to go, but Southend remained well in control and looked much more likely to score.
Wise now has until Saturday to try and make an impact before Southend return for a much more important Championship match.