To set aside a standing rule for this case. An override should leave a trace, since it is an exception someone chose.
Old English oferrīdan (to ride across, trample), from ofer (over) + rīdan (to ride); the old image of riding roughly over ground gave the modern sense of setting aside a standing rule for one case.
The deliberate setting-aside of a standing rule for one case, chosen rather than fallen into by accident. What makes it an override and not a quiet drift is the trace that choosing leaves behind.