Southend, competing in their first ever play-offs, will start next Saturday's second leg as favourites which they will feel is justified after finishing above the Cobblers in League Two and beating them three times before this draw.
Twelve months ago, Northampton all but threw away their chances of reaching the play-off final when they were beaten 2-0 at home by Mansfield and although they took the second leg 3-1, they bowed out on penalties.
This was a predictably tight affair, with chances at a premium although Southend had arguably the best of them 12 minutes from time when substitute Luke Guttridge headed wide from a Freddy Eastwood cross, with the goal apparently at his mercy.
Northampton's leading scorer Scott McGleish was well shackled in the main by central defenders Adam Barrett and Spencer Prior, but he still had his moments.
McGleish will feel he should have opened the scoring in the eighth minute when miscuing a Lee Williamson cross 12 yards out and in the 69th minute McGleish hung in the air before heading a chipped cross by Charlie Hearn agonisingly over the crossbar.
His strike partner Andy Kirk was even quieter, but the former Boston man almost added to his seven goals in nine matches in a Claret shirt just a minute from time.
He was sent dashing clear by Chris Willmott's long punt, but his first touch let him down and his final shot was touched away by Darryl Flahavan.
Flahavan also made an excellent stop three minutes before the break, just seconds after his opposite number Lee Harper had needed to be at his most alert, diving smartly to his right to keep out a header by Mark Bentley from Mark Gower's cross.