The injury-ravaged Shrimpers were two goals down in the opening 11 minutes as Marques and Naylor punished slack marking at corners from the right.
Angolan international Marques climbed to head home Bradley Johnson's sixth-minute corner for his first goal of the season. Then Johnson took a short corner to Andy Robinson five minutes later and his cross was headed in by Leeds-born Naylor, who scored his first goal since arriving on loan from Ipswich this month.
The Shrimpers were so short-handed that they named only four substitutes and Steve Tilson's side suffered a further blow when striker James Walker limped off after 39 minutes.
With Leeds struggling to build on their excellent start, Theo Robinson was only inches away from pulling one back for Southend just after the hour with a powerful drive.
Southend increased the tempo but with Marques and Naylor commanding at the back, they could not find a way through.