The Blues saw off the NPL Premier's second-placed club ahead of the North Riding Senior Cup final at the Riverside Stadium.
It was a depleted Macclesfield side as they rested players ahead of their play-off semi-final with Worksop Town on Tuesday.
Nevertheless, Whitby were professional in the eyes of manager Nathan Haslam.
Stephen Walker netted early in the second half and skipper Danny Rowe, on his 200th appearance headed the winner, eleven minutes from time.
Haslam spoke to Whitby Town TV after the hard-fought win at a windswept Towbar Express Stadium:
The Blues take on Boro Rangers, from Northern League Division One, at Middlesbrough FC, in the North Riding Senior Cup final, on Monday May 13th.


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