After the original game at The Oval the previous Saturday finished in a 2-2 draw, United the midweek trek into Kent with Jack Franklin, Chris Agutter, Grant Harrison and Ben Dartnall all absent from the side that started Saturdays fixture.
Patryk Miszkiewcz made his first ever start in a United top, with Luke Snashall and Casey Ham paired in central midfield and Scott Dartnall slotting in at left back.
From the very first whistle Herne Bay were looking to make home advantage count and use the width of Winch's Field to their advantage as they pressed, but it was United who had the first goalscoring opportunity.
An angled ball from captain Shaun Loft was controlled by Jack Divall, who made space to get away an effort that forced Jack Delo into a diving save.
The effort spurred Herne Bay into life as they enjoyed a 15 minute spell where they attacked with real intent.
Grant Young had to be at his best to deny Danny Lawrence after getting the slightest of fingertips on an 18 yard effort to turn it round the post.
Young denied Lawrence again minutes later, before James Turner and Jordan Casey were guilty of missing good chances for the hosts.
Ryan McBride then warmed the palms of Delo with an effort similar to his goal at The Oval last Saturday.
Divall forced Delo into a smart save with the first half drawing to a close as United were once again at least equal to their higher level opponents.
The second half began and before the half time burgers had been finished, Herne Bay were ahead.
Joe Nelder was allowed too much time and space to curl the ball past Young from just outside the area.
United showed their fighting spirit and resilience, immediately drawing level.
Loft rose highest to head into the path of McBride who slid the ball past Delo as United silenced the home crowd
United now had the bit between their teeth and pushed forward with the belief of scoring again, and they were right.
Jason Taylor, whose pace and direct style caused the Herne Bay defence problems during both matches produced an inch perfect cross for McBride to tee-up Divall to drill home past Delo at the far post.
Many could be forgiven for thinking that a repeat of the first fixture could occur as Herne Bay through bodies forward in an attempt to equalise, but Young comfortably claimed every high ball into the area.
The defence of Miszkiewcz, Loft, Kneller and Dartnall showed great awareness to stifle Bay's attacking intent.
They were ably backed up by Divall, Taylor, Snashall, McBride and Wes Tate who chased the ball down all over the park as United secured victory and a tie at Folkestone Invicta in the First Qualifying Round on Saturday 14th September
UNITED: Young; Miszkiewcz, Dartnall, Loft (C), Snashall, Kneller, Divall, Ham (Marshall), McBride, Tate, Taylor