Whaley picked up a long punt from goalkeeper Simon Eastwood and rifled home a low shot from outside the box to provide a breakthrough that had appeared elusive in a scrappy start.
Grimsby almost levelled five minutes later when Eastwood had to dive full-stretch to keep out Olly Lancashire's header from a corner. The home side rallied for new manager Neil Woods straight after half-time but failed to make the pressure tell.
And the game was virtually sealed when Steve Williams got the faintest of touches to a backward header from Grimsby's Damien McCrory from a few yards to make it two.
A miserable night for the Mariners was compounded when James Hanson drilled past Nick Colgan to seal all three points seven minutes from time.