Super sub Simon Yeo came off the bench to earn a vital point in Lincoln's run for the play-offs.
Things looked bad for the home side when in-form Southend striker Leon Constantine grabbed his 17th and 18th goals of the season just before half time.
But Lincoln hit back six minutes after half time when Franny Green got an acrobatic final touch on a long throw from Gary Fletcher.
The home side surged forward in a desperate attempt to find the equaliser, but looked to be frustrated by a combination of time-wasting from the visitors and the close-range shot from defender Ben Futcher which looked to have crossed the line, but which was not given by referee Alan Penn.
But it was Yeo who sent the crowd home happy went he ran onto a punt forward and steered the ball past Southend keeper Darryl Flahavan.
The goal came four minutes into injury time and referee Penn still found another three minutes in which Southend threatened to spoil the party.
The visitors, looking forward to the weekend's LDV final against Blackpool, made a promising start and dominated much of the first half.
Drewe Broughton had a goal ruled out for offside before the impressive Constantine gave the visitors a 31st minute lead.
The lively striker made the most of a poor back-header from Kevin Ellison and stabbed the ball past stranded Lincoln keeper Alan Marriott.
It got worse for the home side five minutes later when they failed to clear a corner from the left and Constantine made the most of the indecision blasting the ball home from 15 yards out.
Lincoln tried to get one back before half time and were unlucky when Flahavan produced a brilliant goal-line save to deny Fletcher.
At the other end, Marriott mirrored his opposite numbers heroics with a superb one-handed save to deny Lawrie Dudfield.