Dons disappointment on Saturday saw them drop to 15th in League One.
Charlie Kelman netted the only goal of the game after just five minutes to give Southend their first win of the season. Having threatened it in their last two outings, Gary Waddock's side picked up the three points, but they remain in the relegation zone, though leaping AFC Wimbledon. Goals from Abu Ogogo, Jonson Clarke-Harris and Tony Craig ensured they would go down to eighth-placed Bristol Rovers.
After their win over Dons in the week, Ipswich Town took over at the top of League One with a second 1-0 win in a row, beating GIllingham at Priestfield. Previous incumbents Coventry should have played Bury this week, but without a game, they saw Wycombe draw level on points with them after Adebayo Akinfenwa's penalty secured a 1-0 win over Portsmouth at Adams Park as Pompey slip to 20th, jumped by Accrington who drew 1-1 with play-off hopefuls Blackpool.
Bolton got their third point of the season but remain in negative numbers after sharing the spoils with Dons' next opponents Sunderland, while Peterborough's progress was stunted by Doncaster, who ran out 2-0 winners. Rotherham and Shrewsbury drew 0-0, Fleetwood beat Rochdale 2-1 and Burton went down to Tranmere Rovers by the same score.
The biggest score of the day went to travelling Oxford United as they smashed six past managerless Lincoln City at Sincil Bank - a win which lifts Karl Robinson's side into the top half.