It was widely reported that ex-Dutch under-21 striker Prince Rajcomar was getting a trail but he sadly missed his flight from Germany.
But it was still a Southend side full of members of the first team squad, all of whom took part in the defeat at Norwich last week.
The home side dominated the first quarter with James Walker just wide with a free-kick from 20 yards.
Ex-Blue midfielder Luke Guttridge started for Northampton, and nearly gave them the lead with their first real chance as with a header well saved by Joyce.
However, it was the surprising figure of Osei Sankofa who found himself in the perfect position to collect a pass from Dougie Freedman and palce a lovely shot from 12 yards into the left hand corner.
Walker and Sawyer both failed to take further chances after the break before the Cobblers equalised after 60 minutes through Courtney Herbert after a pass from Gutteridge.
Only three minutes had passed when a Lee Sawyer right wing cross allowed Dougie Freedman to restore the Shrimpers lead from close range.
Blues' youth Julian Okai, a half-time replacement for Harry Crawford, shot directly into Cobblers keeper Brown from the edge of the area.
Northampton had already threatened through Guttridge and Herbert when Michael Jacobs just shot wide and Sankofa had another chance for the Blues but hit his shot well over.
Jacobs was not to be denied though and hit a terrific strike from 25 yards into the top right hand corner for the Cobblers equaliser.
Herbert even had a chance to grab a winner in stoppage time but Blues keeper Joyce made a fine save.
Southend United: Joyce, Sankofa, Clayton, Reynolds, Nesbitt, Scannell, Sawyer, O'Keefe, Walker, Freedman, Crawford (Okai 46)
Subs not used: Bentley, Owinja, Milner and Asante.