Team boss Ricky Duncan made two changes from the team that lost to Luton 3-1 last week, even though it remained basically a youth side.
Ade Osifura played at right-back instead of Kane Ferdinand, while Republic of Ireland Under-17 international George Smith replaced trailist Coskun Ekim.
And it was young Smith that handed the Shrimpers the lead with less than a minute on the clock!
A mere 35 seconds had passed when the first-year scholar was allowed to enter the home side's penalty area unchallanged and shoot hard and low into the right-hand corner of the net.
The Borough immediatly went up the other end and just missed out on an equaliser when Jack Cornill 20-yard efford rebounded off the bar and Anthony Jack hitting the rebound well over.
However, it was the Essex boys who continued to look good, wide boy Marcus Milner doing the business, making a good chance for Alex Woodyard.
After Julian Okai tried his luck from 25 yards, Milner was involved again, just missing the goal from Okai's cross.
Stevenage did find the net two minutes from the break, but the former ColU trainee Jordan Pavett's effort was disallowed for offside.
There was still time for Milner forced the Borough keeper Charlie Crowley into making a good save, and then making it a double one when he pushed away Okai's quick follow-up.
The Herts based club were gaining more of the possession at the start of the second half and Pavett nearly took advantage of it, but Duan Ofon-Acheampong headed over from Milner's cross to remind Stevenage it was the away side that were leading.
Okai confirmed this when hitting the post from a James-Lewis lob over the defence, and it was that player who hit the top of the bar with a 30-yard half-volley.
In fact James-Lewis was cursing his luck again soon after when on 72 minutes his header was cleared off the line, however just a couple of minutes later Stevenage were level.
Nikolas Salapatas' free-kick from 25 yards curled over the wall and passed Blues keeper Daniel Bentley on it's way into the top left-hand corner.
So the last 15 minutes saw the young Shrimpers hanging on a touch with Chance O'Neill, Pavett and Salapatas all going close for the Blue Square premier Champions's reserve side, but they could not break through for the winner.
A good point lads in the final game of their Totesport.com Combination East Division season that was won by Watford, with the Shrimpers gaining two wins, five draws, and ten defeats.
A few hammerings as well amongst those losses, but, in the end, with all that's been going on at the club on and off the field, it's lucky that we've been able to complete the fixtures at all!
Southend United: Bentley, Osifuwa, Whittaker, Reynolds, Nesbiitt, James-Lewis, Woodyard (Ferdinand 78), Milner (Furlonge 75), Smith (Hyland 78), Okai, Ofon-Achampong.
Subs not used: Chambers, Baucutt.
League Table (you might want to pass!)
POS P W D L GD PTS
1 Watford 18 13 2 3 30 41
2 Ipswich Town 18 10 3 5 16 33
3 Norwich City 18 9 3 6 14 30
4 Wycombe 18 7 7 4 4 28
5 Peterborough 18 8 3 7 10 27
6 Luton Town 18 8 0 10 -5 24
7 Colchester 18 5 8 5 8 23
8 Northampton 16 4 4 8 -11 16
9 Stevenage 16 3 3 10 -34 12
10 Southend 18 2 5 11 -32 11