Jody Craddock's brave header earned Wolves their first win in five games.
Craddock dived to nod home Michael McIndoe's free-kick but then had to be stretchered off after colliding with Southend defender Efe Sodje.
Freddy Eastwood had the Shrimpers' best chance but fired over in the first half after meeting Simon Francis' long ball.
Wolves saw Jay Bothroyd's shot saved by Darryl Flahaven and McIndoe hit the post from six-yards out before Craddock scored to give his side the points.
Southend assistant manager Paul Brush:
"There aren't any new words we can say to the players.
"It's very tough, confidence is not at its highest right now. Their confidence will only grow with a result. We need a 1-0 win off someone's backside."
On out-of-sorts striker Freddy Eastwood he said: "It's a team game. When we don't create, he doesn't get chances."
Wolves boss Mick McCarthy:
"This game was a turning point for us. We had played 20 games and were nine points from the top and 10 from third-bottom.
"So we asked ourselves 'which way do we want to go?'.
"That was the message beforehand and three points takes us the right way - a defeat and we might have had problems."
Southend: Flahavan, Francis, Sodje, Prior, Hammell, Campbell-Ryce, Hunt, McCormack, Gower (Cole 76), Eastwood (Hooper 75), Bradbury (Harrold 85).
Subs Not Used: Welch, Clarke.
Wolverhampton: Murray, Little, Breen, Craddock (Edwards 64), Clapham, Kightly, Henry, Olofinjana, McIndoe, Johnson (Craig Davies 86), Bothroyd (Clarke 73).
Subs Not Used: Oakes, Potter.
Goals: Craddock 61.
Ref: P Armstrong (Berkshire).