Micky Adams made six changes to Coventry's line-up following their dismal 2-1 Boxing Day defeat to Ipswich.
Andy Whing was recalled from his loan spell at Brighton to feature at right-back and Kevin Kyle partnered Leon McKenzie up front, with Stern John not even featuring on the bench as 16,623 fans gathered at the Ricoh Arena.
The Sky Blues had a let-off in the second minute when Jamal Campbell-Ryce's right-wing cross dropped to Lee Bradbury. The former Manchester City striker turned Robert Page but his deflected shot trickled past a post.
Despite Southend's bright start with their neat passing, it was the home side who showed a cutting edge by taking the lead in the 12th minute.
Darren Currie's corner from the right evaded everyone until it reached Elliott Ward at the far post. The centre-half stroked a fine shot from eight yards into the corner of the net beyond Darryl Flahavan.
In heavy rain, Steve Tilson's men might have equalised in the 28th minute. Campbell-Ryce again deceived left-back Marcus Hall to whip in a cross to Bradbury at the back post, but Whing made a vital block to prevent Bradbury's shot from hitting the back of the net.
The old adage that when teams are struggling they have no luck was again proved in the 44th minute. Southend midfielder Alan McCormack unleashed a fierce angled shot from 12 yards which went through Andy Marshall's legs.
The Coventry keeper made a desperate bid to stop the ball crossing the line and referee Dean Whitestone agreed he had been successful despite the visiting team's howls of protests.
Southend started the second half brightly. Centre-half Adam Barrett surged forward and after exchanging passes with two team-mates he found himself inside the box.
Instead of shooting after turning Page, he delayed his shot which gave the Coventry skipper enough time to recover and block his eventual shot.
Mark Gower forced Marshall to scramble to his left to parry his angled effort and then Stephen Hughes forced Flahavan to make a smart save following excellent work by Michael Doyle, Kyle and McKenzie.
It was no surprise when the visitors drew level in the 53rd minute. Steve Hammell was the creator, laying a pass into the path of Gower, who turned and fired a fierce shot into the net in front of Southend's delirious fans.
The visitors should have taken the lead 16 minutes later when Barrett headed captain Kevin Maher's corner against the bar.
Coventry responded with substitute Jay Tabb sending over a cross and Currie's shot from the edge of the box was tipped over by Flahavan as the teams shared the spoils.