On Stanway Pegasus' artificial surface, the teams were evenly matched with both teams passing the ball accurately, but defences were on top in the early stages. Harwich were playing three at the back with new signing Oakley McNair, Archie Corner and Batuham Macit operating the stystem intelligently.
With play becoming open, Harwich took the lead in the 35th minute with Jack Milne netting with a well-placed shot into the far corner of the net.
Pegasus equalised in the 54th minute when Joel Taylor powerfully headed home at the far post following a corner kick.
It was nip and tuck with the game continuing to be good quality entertainment with both teams intent on playing good football.
As 90 minutes approached, Harwich's Freddy Bethell (pictured) had a free kick diverted onto the post and then cleared from the goal-line.
In added time, with the score still level at 1-1 and both teams searching for a winner, it was a tense finish.
The Shrimpers mounted a well-worked attack and a goal looked likely but substitute Tony Clarke was just unable to make a clean contact and apply the finishing touch.
A draw would have been been a fair result but in the very last seconds of added time there was hesitancy between the Harwich keeper and a defender in clearing and former Shrimper Jack Elvestad stole in to score a poacher's winning goal.
It was a cruel outcome for Harwich but they need not be downhearted, having given a good performance and just missing out by the narrowest of margins.
Harwich team: Thomas Maurer, Batuham Macit, Oakley McNair, Archie Corner (captain), Rory Breen, Solomon Griffiths, Freddy Bethell, Alex Pryke, Jack Milne, Harry Tuck and Cody Harrison. Substitutes: Jamie Beecham, Oscar Warnes, Archie Rogers-Bell, Tony Clarke and Joseph Simmons.