It is very hard to prove a negative, but I don't see any evidence that this line is a quote. Nothing similar seems to occur in the Bible, and Novinha, being brought up in a Catholic world, would probably have recognised and noted the allusion anyway. I have also not encountered anything similar in Mormon scripture (relevant as this is Card's own religion), or in general literature. So it seems entirely reasonable to believe that Card came up with the phrase himself.
As to the scriptural style, I think that comes down to the language lesson Card gives the reader in this section. Like many Romance languages, Portuguese has two forms of the pronoun "you": the polite form "você" which takes the third person form of the verb, and the informal "tu" which takes the second person (there is also an even more respectful way of addressing someone formally, as "o Senhor").
Novinha tries to insult Ender by addressing him in the "tu" form:
"vai fora d'aqui, nao tens direito estar em minha casa!" ... she had
spoken to him derisively, using the insultingly familiar tu for "you"
instead of o Senhor or even the informal voce. It was the way one
spoke to a child or a dog.
and Ender replies to her, also using "tu":
"Nao es estrago," he whispered, "es solo fecundo, e vou plantar jardim
(i.e. using "tu es" rather than "você é").
This distinction is lost in modern English, but existed previously with the usage of "thou" as the familiar form of "you". So rendering the translation as "Thou art fertile" is a way of maintaining the usage of the informal pronoun rather than the formal one. Since "Thou" is almost only encountered these days in prayers and translations of the Bible, it has the side-effect of making the line sound scriptural.