The Blues were edged out by Lincolnshire side Gainsborough Trinity, on Tuesday.
Town had started well under joint-bosses Jason Kennedy and Lee Bullock.
They took a deserved lead, on 23 minutes, when Layton Watts' near-post corner was flicked on by Frankie Whelan for Matty Tymon to slam home.
However, Gainsborough levelled in first-half injury time when long ball wasn't dealt with by the Whitby backline.
The visitors were buoyed by this and won it right at the death with a shot through a crowd of players passing an unsighted Isaac Allan.
Whitby Town TV's Liam Ryder caught up with Bullock at full-time:
Whitby are back in action, away at Bamber Bridge, on Saturday, in NPL Premier.


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