Pegasus mounted an attack straight from the kick-off and immediately won a penalty kick. However, Tom Lewis' effort blasted against the crossbar and went over the top for Harwich to escape.
With 12 minutes gone, Pegasus went down to 10 men when Dylan Ketley-Gregan received a straight red card for a tackle on Alfie Smith and was dismissed.
It became a physical encounter now and, with a good crowd present, there was an exciting cup-tie atmosphere.
Pegasus, who knew a draw would be good enough to secure the runners-up spot in Division One North, were dangerous on the break and Harwich goalkeeper Brad Cook was forced to make an excellent diving save to keep out Harry Pinkney's low shot which was heading for the corner of the net.
Pegasus were getting players back in numbers behind the ball and Harwich were finding it difficult to create clear-cut openings so half time arrived with the match goalless.
Soon after the interval, a quick Pegasus break caught Harwich pushing forward again and short of defenders. Although Cook pulled off a good stop, the ball came out to Kieran Williams and he gave a jubilant Pegasus the lead.
Pegasus continued to frustrate Harwich, whose best effort was a scorching long-range effort from Luke Mayhew (pictured) that skimmed the angle of post and crossbar.
Harwich were constantly pushing forward and, at times, leaving a lone defender to cope with Pegasus breaks and Cook was called upon to pull off another diving save.
After the midway stage of the half, Harwich pressure produced an number of corners and goalscoring opportunities but former Shrimpers goalkeeper Sam Felgate and his defenders refused to concede.
In the closing stages, Harwich had their best chances but Jack Wood's shot and Alfie Eldridge's header were thwarted by superb blocks by the Pegasus defenders.
The final-day results mean home play off semi-finals on Saturday (April 26) for Pegasus against Diss Town and Harwich, who entertain Framlingham Town. The Shrimpers' third-place finish is their highest in a division of senior football since the 2003/04 campaign which ended in promotion.
There is still all to play for, so let's get behind the Shrimpers again in these promotion deciders.
Harwich team: Brad Cook, Alfie Smith, Jack Wood, Dan Keeble, Reece Harte, Tyler Sullivan, Alfie Eldridge, Gareth Heath (captain), Luke Mayhew, Luke Spurling and Louie Bloom. Substitutes: Keelan Milburn, Liam White, Alfie Canning (all used), Oakley McNair, and Will Crook (not used).