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Boro came from 1-0 down in the Yorkshire Coast derby at the Flamingo Land Stadium.
Whitby took the lead from the penalty spot 11 minutes into the match through Jacob Hazel.
Scarborough Captain Michael Coulson levelled for the home side on 26 minutes.
Nathan Cartman scored the winning goal on 82 minutes, heading in from close range from an Ashley Jackson cross.
It was an entertaining encounter for the 600 fans watching, 510 from Scarborough and 90 from Whitby. 600 is the maximum allowed due to the COVID-19 restrictions.