Brad Cook (pictured) was called into action early, stopping a shot from Marko Protic.
However, he could not prevent the hosts taking the lead in the 24th minute.
A low ball in from the right found Archie Hammond in front of goal and although Cook stopped his initial effort, the rebound was prodded home.
Harwich tried to respond and Joe Knight went close to a quick equaliser.
He wriggled away from Mark Twumasi and struck a low shot which was pushed away for a corner at the foot of the post by keeper Fred Burbidge.
It was the closest the visitors were to come to a goal despite it being a fairly close half.
At the other end, Ollie Fernandez saw his header saved by Cook shortly before half time and the Shrimpers went in a goal down.
A good move effectively ended the visitors’ chances on the hour mark.
Winger Yannis Mengou found Nathan Sollosi in the centre and he pushed the ball on for Protic to slot beyond Cook.
Harwich keeper Cook, who has played every game this season, ensured the scoreline remained at 2-0.
Zac Pedro did well to stop Sollosi’s header from a corner on the line and Cook then clawed the ball to safety.
And in the closing stages, the 24-year-old stopper pulled off a good save low to his right to prevent Mengou adding a further goal.
The victory booked Buckhurst Hill’s place in the end-of-season play-offs and they will now aim to move up to Step 4 in the next couple of weeks.
Harwich, meanwhile, are assured of a 13th-place finish in their inaugural Essex Senior League season.
The Shrimpers complete their campaign on Saturday (April 25) with an away game against relegation-threatened Romford, who play at Barking (kick-off 3pm).
Harwich team: Brad Cook, Oakley McNair, Charlie Canham, Jack Wood, Tiwa Odufuye, Liam White, Jenson Goode, Zac Pedro, Alfie Canning, Louie Bloom and Joe Knight. Subs: Luke Hopwood, Mo Hashemi and Jeremiah Ajisafe (all used)