The dispel magic spell targets magical effects, not their points of origin
The dispel magic spell states:
Choose one creature, object, or magical effect within range. Any spell of 3rd level or lower on the target ends. [...]
So while the caster of dispel magic could not target the artifact itself because antimagic field states:
[...] Spells and other magical effects, such as magic missile and charm person, that target a creature or an object in the sphere have no effect on that target. [...]
This does not prevent the caster of dispel magic from targeting the magical effect that is outside of the antimagic field. Thus the caster could target the portion of holy aura that it outside the antimagic field, thereby ending the spell without ever needing to target its point of origin, which cannot itself be targeted.
A rather unrelated sidenote, there are times in the rules where a magical effect can be dispelled without having to target its point of origin (besides dispel magic): the darkness and daylight spells:
If any of this spell's area overlaps with an area of light created by a spell of 2nd level or lower, the spell that created the light is dispelled.
If any of this spell's area overlaps with an area of darkness created by a spell of 3rd level or lower, the spell that created the darkness is dispelled.