Goals from Luke Guttridge and Mark Gower fired the Shrimpers to all three points, and the top of the table ahead of Saturday's games.
Barnsley maintained their play-off push with a win at Nottingham Forest - Micah Richards got both goals in a 2-0 success.
Scunthorpe are guaranteed to drop at least one place on Saturday, despite not being in action, as Hartlepool and Blackpool clash at Victoria Park - though it is also impossible for the Iron to drop into the bottom four.