undef $hashRef should do the trick, I'd think.

Yes, that would undef the reference itself — but that might not necessarily lead to the hash being undefined (which I think is what the OP is after...).  undef %$hashRef, OTOH, would undefine the hash being referenced.

But I suspect the real question here is "why is the associated memory not being freed?" :)   If so, circular references (in data structures held in the hash) might be the reason...  Object::Destroyer might help in this case. Also see Re^3: Large Memory for a list of related modules that might help with locating circular references.