The tie finished 1-1 at the end of normal time after Tom Pett’s strike ten minutes after half-time was cancelled out by a Ryan Leonard goal 12 minutes later.
However, after Barry Corr had hit the crossbar with a last-minute penalty, Phil Brown’s side booked their place in the final against Wycombe thanks to extra-time goals by Stephen McLaughlin and Michael Timlin.
Stevenage almost got off to a dream start when Ben Kennedy fell in the box under a clumsy looking challenge from Ben Coker, only for referee Graham Scott to wave away the visitors’ protests.
However, if Stevenage thought themselves unlucky not to have been awarded a spot-kick for that incident, then Southend were also more than a little unfortunate not to have been given a penalty when Simon Walton clearly prevented Corr from reaching a corner after just seven minutes.
In an opening half in which there were few goalscoring opportunities, it was the home side who had the clearest chances, the first coming on the quarter-hour mark following a great move down the left flank involving David Worrall and Corr.
But after the former had given his team-mate a clear sight of goal, his close-range shot was beaten to safety by Stevenage goalkeeper Chris Day at his near post, before Joseph Pigott nearly gave his side the lead with a sweetly struck shot from just outside the area.
The best opening, however, fell the way of Corr a minute before half-time, but after working himself space in a crowded penalty area, the striker chipped his shot wide of Day’s near post when it seemed easier to score.
And Southend were made to pay for their profligacy in front of goal when Pett fired Graham Westley’s team in front after 55 minutes, although their goal was more than a little lucky.
Having worked a corner short between Walton and Parrett, the latter’s shot from the edge of the area took a deflection off Wells, before falling kindly at the feet of Pett, with the substitute side-footing home from close range.
However, Southend did not take long to draw level, with substitute McLaughlin’s deep cross from the left flank somehow finding its way through to an unmarked Leonard at the back post, and he made no mistake with a confident finish from close range.
Thereafter, it was the home side who looked the most likely to score a winner in normal time, only for Pigott miss two good chances, before there was drama in second-half injury time when referee Scott adjudged Dean Parrett to have pushed over Leonard in the box.
The decision looked harsh and justice was arguably done when Corr struck the top of the bar with his 97th-minute spot-kick, taking us into an extra half an hour, 30 minutes which Southend again dominated as their opponents tired visibly.
After Day denied both McLaughlin and Corr with impressive saves, Southend finally scored the goal their pressure merited when with only 12 minutes left to play, McLaughlin headed home John White’s inch-perfect right-wing centre to send the home fans into a state of delirium.
And that only increased when Timlin won back possession on the edge of the Stevenage box, before jinking his way past a posse of opponents and curling an unstoppable effort past Day to seal the Shrimpers place at the home of football against Wycombe Wanderers on May 23.
Watch the League Two play-off final between Southend and Wycombe live on Sky Sports 1 HD on Saturday 23 May from 5pm.