In the 12th minute, Harwich's Ewan Livingston created the first scoring chance when he set up Alfie Canning who fired his shot wide.
The Shrimpers had made a good start and were rewarded five minutes later when last season's leading goalscorer Luke Mayhew netted direct from a corner kick.
Canning was leading the Harwich attack and, following a cross, this time he was only inches off target with his shot.
With 25 minutes gone, Clacton came back and were unlucky with a shot that struck the Harwich crossbar.
It was an open game with both sides playing attacking football and Harwich creating plenty of chances. Mayhew's well-taken free kick went close with the keeper beaten and later Livingston's fierce drive went just over the crossbar.
The Harwich defence were troubled by Clacton's speedy attackers and before half time the Seasiders equalised when Jaiden Hanna's shot took a deflection, giving the wrong-footed Shrimpers goalkeeper Brad Cook no chance.
The second half proved to be a much tighter and more physical affair with both teams using their substitutes and, in contrast to the first period, there were no real scoring opportunities.
With the teams having cancelled each other out at the end of the 90 minutes, a penalty shoot-out was necessary to determine the winners.
With Harwich having taken a 3-2 lead, Cook saved Clacton's third penalty and in the end, having taken five perfect spot kicks, the Shrimpers ran out 5-3 winners.
Harwich team: Brad Cook, Freddy Bethell, Dan Keeble, Will Crisell, Reece Harte, Tyler Sullivan, Brandon Rusby, Liam White, Luke Mayhew, Alfie Canning and Ewan Livingston. Substitutes: Harry Tuck, George Tuck, Alfie Smith, Tony Clarke and Jack Elvestad (all used)
- In the match day programme Shrimpers chairman Tony Armstrong referred to Kevin Beattie as probably the most famous player to wear the black and white stripes, a person who always had time for the fans in his two-season spell at Harwich during which he netted 28 goals in 50 appearances. Tony, who was manager during that period, said: "Thanks for everything you did for me Beat, my family and everyone at Harwich & Parkeston FC. RIP Kevin Beattie. Your legendary status will live on for many years."