Swindon got off to a perfect start scoring almost straight away after a long distance Andy Nicholas shot was only half saved and Simon Cox was on hand to score from close range with the rebound making it 2-1 after 2 minutes.
Southend then hit the bar with a cross, but it hit the top of the bar and went off.
Southed should have been given a free kick for offside, but instead play was allowed to continue and then Aljofree fouled Clarke on the edge of the area, and a free kick was given to Southend. The kick found Barrett who headed in making in 1-1 after 32 minutes.
Swindon had a lot of the play during the second half and the game seemed to be heading towards a 1-1 draw when with 2 1/2 minutes of stoppage time played Mark Gower scored from close range giving the Essex side a 2-1 win.
Overall it was a poor result for Swindon who played well and should have at least got a draw out of the game. The defeat leaves Swindon in 14th place ahead of next Saturday's game at home to Brighton.