This is from a text of 1580, "Antiguas costumber del Perú", by the indigenous Peruvian Jesuit author Blas Valera. It's easier to understand if you look at the sentence or two before this. Valera has just been saying that in former times the Vilahoma, the leading minister of the Inca religion, was a kind of "pontífice máximo", "que en los tiempos antiguos tenía jurisdicción sobre los reyes; aunque después de Topa Inca Yupanqui dieron una baja muy grande él y los demas ministros [...]".

See https://books.google.es/books?id=g1HmfGCvktUC&pg=PA37&lpg=PA...

"Baja" here is being used in the sense of a diminution. Here is its definition in the first RAE dictionary (1726):

"Baxa. s.f. Diminución del precio, valór y estimación de alguna cosa."

So "dar una baja" means to suffer or undergo a diminution. Here, it means that from this point on the power and authority of the Vilahoma and other ministers of the Inca religion, formerly greater than those of the king himself, were greatly reduced, as were their nobility and wealth.