Ordo verborum est, ut te et quem misisti Iesum Christum cognoscant solum verum Deum.
which may be translated as,
The right order of the words is: “so that they may know you and whom you sent, Jesus Christ, [as] the only true God.”
There is actually no question about the order of the words. The Greek text was plainly visible for him and others to see.
Γʹ αὕτη δέ ἐστιν ἡ αἰώνιος ζωή ἵνα γινώσκωσιν σὲ τὸν μόνον ἀληθινὸν θεὸν καὶ ὃν ἀπέστειλας Ἰησοῦν Χριστόν TR, 1550
The Greek text simply does not corroborate Augustine’s Latin translation of the Greek text. One should also note that the Vulgate does not exhibit Augustine’s word order, either.2
If the Greek text had stated, τὸν μόνον ἀληθινὸν θεὸν σὲ καὶ ὃν ἀπέστειλας Ἰησοῦν Χριστόν (“the only true god, you and whom you sent, Jesus Christ”), then he might have a basis for his argument. However, look closely at the Greek text. σὲ by itself precedes τὸν μόνον ἀληθινὸν θεὸν, and therefore, τὸν μόνον ἀληθινὸν θεὸν (“the only true god”) alone is in apposition to σὲ (“you”).
Why, then, did Augustine make such an assertion? He was unable to explain John 17:3 as it stood in the Greek text.
Heinrich August Wilhelm Meyer wrote,3
Although τ. μόν. ἀλ. θεὸν refers solely to the Father, the true divine nature of Christ is not thereby excluded (against the Arians and Socinians, who misused this passage), all the less so as this, in accordance with His (Logos) relationship as dependent on the Godhead of the Father, forms the previous assumption in ὃν ἀπέστειλας, as is certain from the entire connection of the Johannean Christology, and from ver. 5. Hence it was unnecessary,—nay, even a perversion of the passage, and running counter to the strict monotheism of John, when Augustine, Ambrose, Hilary, Beda, Thomas, Aretius, and several others explained it as if the language were: ut te et quem misisti Jesum Christum cognoscant solum verum Deum. Only One, the Father, can absolutely be termed the μόνος ἀληθ. θεός (comp. ὁ ὢν ἐπὶ πάντων θεός, Romans ix. 5), not at the same time Christ (who is not even in 1 John v. 20 the ἀληθινὸς θεός), since His divine entity stands in the relation of genetic subsistence to the Father, i. 18, although He, in unity with the Father, works as His commissioner, x. 30, and is His representative, xiv. 9, 10.
1 PML, Vol. 35, p. 1904, Tractatus CV, 3.
2 haec est autem vita aeterna ut cognoscant te solum verum Deum et quem misisti Iesum Christum
3 Meyer, p. 462
Aurelius Augustinus Hipponensis. “In Joannis Evangelium Tractatus CXXIV.” Patrologiæ Cursus Completus: Series Prima. Ed. Migne, Jacques Paul. Vol. 35. Petit-Montrouge: Imprimerie Catholique, 1845.
Meyer, Heinrich August Wilhelm. Critical and Exegetical Handbook to the Gospel of John. Trans. Urwick, William. Ed. Crombie, Frederick. New York: Funk, 1884.