The Shrimpers eased into an early lead with first-half strikes from Mark Bentley and Wayne Gray.
They now move onto 74 points - leapfrogging Yeovil who are on 71 points ahead of Saturday's games.
Scunthorpe are third with 68 points, above Swansea by virtue of goal difference.
If United lose to Macclesfield on Saturday, they will drop out of the top three for the first time all season.