Early Harwich pressure almost resulted in a goal when a Borough defender, in attempting to clear, headed against his own crossbar and Shrimper Danny Garrad also came close to scoring on two occasions.
Borough weathered the storm and came back, forcing Shrimpers goalkeeper Brad Cook to make a good diving save.
With 15 minutes gone, Harwich mounted a well-worked 5-man move that culminated in Alfie Eldridge giving them the lead with a clinical finish.
Two minutes later, Harwich scored their second goal when Borough keeper Zak Tovey did well to push out Liam Riley's goalbound shot but the alert Garrad followed up to net.
With half time approaching and Harwich seeking their 3rd goal, Tovey produced a super save to tip Louie Bloom's 25-yard piledriver over the crossbar.

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After the break, Harwich could not recapture their smart passing football of the first half and the young Borough team proved to be a force to be reckoned with.
With 70 minutes played, Borough reduced the arrears with skipper Milo Barton neatly placing his header into the corner of the net.
Harwich needed that 3rd goal to give them a cushion now and it came in the 80th minute from the busy Garrad, who netted his 15th goal of the season when he made a run to the edge in of the 18-yard line before curling a superb shot into the far corner of the net.
Borough were not done and in added time Theo Goddard scored his team's second goal with a well-placed shot that again gave Cook no chance of saving.
It was proving a nervy finish for Harwich and their supporters but with central defender Jack Wood their man of the match, the Shrimpers successfully saw out the remaining minutes.
With Stanway Pegasus dropping 3 points elsewhere, Harwich had strengthened their position in second place in the league table.
Harwich team: Brad Cook, Keelan Milburn, Jack Wood, Dan Keeble, Reece Harte, Alfie Smith (captain), Alfie Eldridge, Liam Riley, Greg Rodger, Louie Bloom and Danny Garrad. Substitutes: Brad James, Tyler Sullivan, Liam White (all used), Cody Harrison and Gareth Heath (not used).