Lee Barnard's fifth goal of the season after 47 minutes earned the Blues the points, but they should have won by a more convincing margin.
Walsall had one shot on target and created little as they extended their run to just one victory in their last seven games.
Neither side had a chance on target in the first half, but it was the home side who created the better chances.
Southend should have taken the lead in the 14th minute when James Walker burst into the box and shot wide with the Walsall defence trailing in his wake.
Mark Gower was denied after 44 minutes by the woodwork when his 30-yard right-foot rocket bounced off the underside of the bar and bounced to safety with keeper Clayton Ince beaten.
Walsall manager Richard Money brought on Stefan Moore and Alassane N'Dour at half-time to pep his team up, but three minutes later Southend took the lead.
Gower released Charlie Mulgrew whose cross into the box took a deflection off Anthony Gerrard before Barnard got the final touch.
The Shrimpers continued in the ascendancy with Gower and Barnard both firing straight at keeper Ince.
Ince turned a 25-yard Simon Francis shot over, while Gerrard cleared another Walker effort off the line before sub Moore saw Walsall's only shot on target safely held by keeper Darryl Flahavan.