Dan Harding scored the only goal for Southend to hand his former club their third league away defeat in a row.
The defender curled a free-kick into the top corner after 18 minutes.
The hosts should have made it 2-0 but Casper Ankergren parried a Francis Laurent's effort and Hal Robson-Kanu blasted over from a good position.
Neil Kilkenny was denied by keeper Adam Federici, while substitutes Andy Robinson and Robert Snodgrass also went close for Leeds.
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Subs Not Used: Walker, Sankofa.
Goals: Harding 18.
Leeds: Ankergren, Richardson, Michalik, Telfer, Parker, Kilkenny (Robinson 67), Howson, Douglas, Delph (Snodgrass 67), Beckford, Becchio. Subs Not Used: Lucas, Prutton, White.
Booked: Michalik, Becchio, Robinson.
Att: 10,132
Ref: Pat Miller (Bedfordshire).
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