The kick-off was delayed by 15 minutes following a traffic accident near the ground and when play did get underway both sides struggled to create openings.
Both enjoyed spells of possession but it was the visitors, who went into the match unbeaten away from Hillsborough in the league, who edged it.
Their best chances early on came from dead ball situations, with Frankie Simek and Burton O'Brien both firing across the face of goal. Glen Whelan came closest to breaking the deadlock on 21 minutes when he thumped a right foot shot against Darryl Flahavan's crossbar from the edge of the box after being set up by Deon Burton.
Southend responded immediately with four-goal topscorer Freddy Eastwood firing over the bar and Mark Gower heading narrowly wide from a Steven Hammell corner.
The Shrimpers' goal continued to lead a charmed life on 28 minutes when Whelan again hit the crossbar from O'Brien's free kick before Lloyd Sam blasted the follow-up over.
Southend had the last say of the half with Eastwood latching on to a Gower ball to fire just wide with a diving Brad Jones beaten.
Whelan forced a save out of Flahavan with a glancing header as the second half got underway, but it was Southend who looked the better side.
Their neat attacking play nearly reaped dividends when skipper Kevin Maher's 18 yard shot was saved by Jones.
Gower then volleyed over the goal after swapping passes with Jamal Campbell-Ryce.
But the best chance fell to Luke Guttridge, who saw his 25-yard effort turned over the bar by Jones.
Owls boss Paul Sturrock shook things up on the hour by introducing Lee Bullen and Chris Brunt, and the latter went close with two shots from distance before having a good effort saved by Flahavan.
Wednesday had a good shout for a penalty late on for an apparent hand ball, before the whistle went to leave them with two draws and two wins on the road in the league.