There were tears all around St James' Park as Exeter dropped out of the league for the first time in the club's long history.
Swansea's victory against Hull had already condemned Exeter to the Conference and the Grecians were strangely lacklustre against Southend.
The players knew they were already relegated by the time Steve Flack struck Exeter's winner in the last minute.
The players were consoled by supporters who ran on to the pitch on the final whistle and there was devastation throughout the ground.
Kick-off was delayed by 15 minutes to allow hundreds of fans queuing outside the ground to filter into the ground.
City keeper Kevin Miller rescued Exeter in the seventh minute when he kept out Tes Bramble's penalty.
Phil Baker's rash challenge on Brett Darby was worthy of a penalty, but Miller stood firm to keep out Bramble's spot-kick.
Exeter were in danger of being overawed by the occasion and failed to muster a single attack in the first 20 minutes.
Flack eventually forced Darryl Flahavan to make a save with a weak shot from 12 yards.
James Coppinger finished off a neat move with a shot from the edge of the box, but again the goalkeeper was equal to the task.
Carl Pettefer should have put Exeter ahead with a close-range shot after the break but his effort was well saved by Flahavan.
Flack headed Justin Walker's corner past the post, then had a header saved from Baker's cross, but time was running out for Exeter.
In the 90th minute Glenn Cronin found Flack, who took the ball around the goalkeeper and fired home from a tight angle.
Exeter boss Gary Peters said: "Everyone is devastated and there is nothing I can say to lift the players. The worst thing is for the fans, because they have lost their Football League club."