Dean Parrett gave Stevenage the lead early in the second half with a fantastic long-range strike.
But Barry Corr’s deflected header on the hour mark drew Southend level and they will now fancy their chances of finishing the job at Roots Hall in four days and booking a trip to Wembley.
The visitors went close to taking an early lead when Michael Timlin poked Corr’s cut-back inches wide.
However, Timlin’s evening came to a premature end shortly afterwards, when a sickening clash of heads with Bira Dembele left the midfielder soaked in blood from a gaping wound above his eye.
Worryingly, Dembele appeared to have been knocked out and was motionless on the ground, receiving treatment for seven minutes.
But while Timlin departed the action for 15 stitches, Dembele played on in a bandage until he was substituted at half-time.
Next to hit the deck was Boro goalkeeper Chris Day following a collision with Stephen McLaughlin, and suddenly all eyes turned to the Stevenage bench where, due to a spate of injuries, 56-year-old goalkeeping coach Dave Beasant had been named among the subs.
The former Wimbledon and Chelsea keeper climbed out of the dug-out to indulge in some gentle stretches, to the delight of the crowd, but Day was eventually able to play on.
Day – himself 39 – ensured the sides went in level at the break when, during nine minutes of stoppage time, he pulled off a fine save with his legs to keep out Dave Worrall’s close-range shot.
However, six minutes after the interval the deadlock was broken when Parrett, who once cost Tottenham £1million as a 15-year-old, curled in a superb shot from 20 yards which flew over Southend keeper Dan Bentley into the top corner.
Southend hit back nine minutes later when Corr’s header from McLaughlin’s corner found its way past Day at the far post.
Day had to turn away a fierce John White drive and Bentley palmed Ben Kennedy’s shot clear to leave the tie finely balanced ahead of Thursday’s return leg.