There were few fireworks for Gary Liddle's men as the Blues suffered a rare home defeat.
It was just a second defeat at the Towbar Express Stadium under Liddle, who took over as Town boss in October.
Strong wind, particularly in the first half, made for tricky conditions.
As can be seen on the match highlights:
Visitors Stockton Town, going well in the first season at NPL Premier level, led with 20 minutes left.
Adam Gell was then sent off for the second match in a row and the hosts quickly made their extra man count to net a second.
Liddle spoke to Whitby Town TV after the match:
A ridiculously-congested league table sees Town in the top-half, in 11th, but only four points clear of the relegation zone.
They return to action, on Saturday, at Preston side Bamber Bridge.


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