The previous line shows “Fili”:
Domine Fili unigenite, Jesu Christe,
Domine Deus, Agnus Dei, Filius Patris,
qui tollis peccata mundi, miserere nobis;
I can’t imagine there are metrical considerations that force the variant form for Vocative.
I’m not sure if the original Greek is available. The modern Greek version (I found on Wikipedia) shows the same variation in case. So here “Filius” and maybe “Agnus” are in Nominative in apposition to the subject.
“Oh Lord Jesus Christ, oh only begotten Son, oh Lord God, you are the Lamb of God, you are the Son of the Father, who take away the sins of the world, have mercy on us.”