Chichester suffered a third straight league loss courtesy of Hythe substitute Jack Mayhew’s strike with two minutes of normal time to go.
A second half double from Hass Ibrahiym condemned Chichester to back-to-back defeats this week.
Herne Bay skipper Laurence Harvey grabbed the winner deep into stoppage time to settle this lively Isthmian south east encounter at Oaklands Park.
Chichester City Women scored two goals in three minutes to win 2-1 at Milton United on Sunday.
Lloyd Rowlatt scored the only goal of the game as Chichester ground out back-to-back league wins in the same week for the first time this season.
First half goals from Callum Overton and Lloyd Rowlatt, and a resilient defensive display after the break, helped Chichester to an impressive win against in-form Burgess Hill.
Chichester City Women bounced back to winning ways with a 2-0 win over AFC Stoneham at Oaklands Park on Sunday.
January ended for Chichester, as it began, with a 1-0 defeat against a fellow Sussex side.
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An 81st minute Lloyd Rowlatt equaliser snatched a point for Chichester against county rivals Whitehawk in a frenetic match that Hawks boss Ross Standen described as a “basketball game”.
