Ethan Embury put the Step 4 Cannons in dreamland with a 32nd-minute opener, only for Jack Hazlehurst to equalise for Chorley just before the break.
Hythe held their own after the break but the National League North side ensured there was to be no shock with Jack Sampson netting the winner 16 minutes from time.
“We showed guts and desire to win it, if you don’t show togetherness and willingness you’ll get nothing here today,” said Chorley’s boss Andy Preece.
“It was a difficult surface and both teams had to play in a certain way, cancelling each other out early on.
“We had our best 10 minutes towards the end when we scored. It gave us belief as we had to scrap.
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