
New signing from Scarborough Athletic, Michael Woods, scored what proved to be the decisive goal as he netted on debut to lift Gary Liddle's side into 16th place.
The reverse fixture, Liddle's second in charge back in October, ended in a goalless stalemate at the Towbar Express Stadium, but this was a much more open affair in Staffordshire.
In recent weeks Whitby have made a habit of having slow starts to game but this time it them to started brightly. In the second minute, Sam Collins - in the starting eleven in place of Jassem Sukar - swung in an inviting cross which just evaded both Matthew Tymon and Nathan Thomas.
Then, twelve minutes later, the flag stayed down against Layton Watts who lay the ball off to Thomas who ventured towards goal only to be denied by a vital last-ditch defensive challenge.
Julius Ndene fired wide from point-blank range to let Whitby off, but it was the visitors who continued to be on top with Watts aiming for Haswell at the back post, only for the ball to drift agonisingly away from his reach.
Shane Bland was the star of one of the first half moment's as he made a crucial save to keep out Hayden Campbell at close range in the 34th minute.
Whitby then struck first, as Aaron Haswell, on as a first-half substitute in place of the injured Thomas, latched on to Bland's flighted ball forwards to prod home past the on-rushing Dino Visser.
Haswell could and perhaps should have added a second before the break as he was played in on goal by Woods, but Visser anticipated his effort well to make the save.
The home side started the second half strongly, just as Whitby had the first, and they thought they were level in the 51st minute only for Louis Potts to be denied by the offside flag in a decision which sparked controversy around the F. Ball Community Stadium.
But on the hour mark, the Seasiders were pegged back. Liam Buckley floated an inviting ball into the box which Campbell stooped to get onto the end of to head home an equaliser.
Lewis Hawkins lined an effort up from distance as Liddle's side looked to mount a response, however he was unable to hit the target, while Woods and Tymon were both prevented from putting Whitby back ahead with Leek defending deep now.
December signing Tymon had also curled an effort inches over the bar just before this duo of changes as Whitby put Leek under pressure after conceding the equaliser.
However, with full time approaching, new signing Woods put Town ahead from the edge of the area. Watts again centred and despite there being a number of Leek defenders present, Woods was able to find the bottom corner.
After getting their noses back in front, Whitby defended strongly and gave Leek little to work with in an attacking sense as the visitors saw the game out to claim a crucial three points.