I don’t know about earliest, but a very obvious place where this doctrine plays a starring role is in the thought of St. Anselm of Canterbury (1033-1109).

Anselm is best known today for his forceful presentation of the ontological argument, one of the seminal arguments in all of western philosophy. That argument goes something like this.

God is “that than which a greater cannot be thought”; in other words, he is a being so great, so full of metaphysical oomph, that one cannot so much as conceive of a being who would be greater than God. The Psalmist, however, tells us that “The fool has said in his heart, ‘There is no God’ ” (Psalm 14:1; 53:1). Is it possible to convince the fool that he is wrong? It is. All we need is the characterization of God as “that than which a greater cannot be thought.” The fool does at least understand that definition. But whatever is understood exists in the understanding, just as the plan of a painting he has yet to execute already exists in the understanding of the painter. So that than which a greater cannot be thought exists in the understanding. But if it exists in the understanding, it must also exist in reality. For it is greater to exist in reality than to exist merely in the understanding. Therefore, if that than which a greater can be thought existed only in the understanding, it would be possible to think of something greater than it (namely, that same being existing in reality as well). It follows, then, that if that than which a greater cannot be thought existed only in the understanding, it would not be that than which a greater cannot be thought; and that, obviously, is a contradiction. So that than which a greater cannot be thought must exist in reality, not merely in the understanding.^1

Let’s unpack this a bit. First, we have the idea (or concept) of a “greatest possible being” or a being greater than which cannot be conceived, as even an atheist (the “Fool” of the Psalms) will surely admit. Now, a being which exists is greater than one which does not: Existence, to Anselm, is a perfection. So it follows that this greatest possible being must actually exist; indeed, it exists necessarily.

So what does this have to do with the modern notion of God? Well, a “greatest possible being” will contain all perfections whatever. This would include being (i) all-knowing, (ii) all-powerful, and (iii) all-good. And it is for this reason that Anselm takes his argument to prove the existence of God. This is all pretty much in line with a scriptural conception of God as well; even if scripture does not explicitly state that God has all these attributes in so many words, it is extremely natural to think of God as being the “ultimate reality” or a “perfect being” or something along those lines.

The ontological argument of Anselm became something of a cornerstone of Christian philosophy and theology. Later, early modern thinkers like Descartes would also endorse a version of the argument. And while the early modern period also saw trenchant critiques (notably from Kant), the argument retains some core of plausibility and folks defend it down to the present day. Perhaps the best modern version of the argument comes from the work of Alvin Plantinga.^2 This argument is not widely accepted today, but still attracts a fair amount of philosophical discussion.^3

So basically, the upshot of this is that omniscience, omnipotence, and omnibenevolence actually just fall out of thinking about God as “the greatest possible being”, a natural enough conception that was reinforced by the philosophical interest in (an utility of) the concept. Interestingly enough, you don’t really even need any sort of appeal to scripture to get this sort of thing going. Considering what a “greatest possible being” would be like is a natural enough philosophical project, and appears to lead to a consideration of a God-like being. Moreover, this sort of conception allows for a particularly forceful argument in favor of God’s existence, an argument that seems to tell against even those who deny the authority of scripture, so emphasizing this conception and argument were natural moves if you were looking to formulate and defend the Church against detractors.

*Edit: I originally (and incorrectly) said that St. Thomas also endorsed the ontological argument, but this was incorrect. While St. Thomas does discuss the argument at some length, he ultimately comes down against it on the grounds that (i) some do not understand God to be equivalent to the "being greater than which none other can be conceived" and (ii) that the proper conclusion to Anselm's argument is that God must exist not actually but merely mentally. So my bad for originally face-planting on that; I underestimated the fallibility of human memory. Thanks to /u/Torin_3 for catching my mistake.

Sources

1. Stanford Encyclopedia of Philosophy: St. Anselm

2. Plantinga, A., 1974, The Nature of Necessity

3. Stanford Encyclopedia of Philosophy: Ontological Arguments. See especially the excellent bibliography for further reading.