Objection 1. It would seem that human souls were created together at the beginning of the world. For it is written (Genesis 2:2): "God rested Him from all His work which He had done." This would not be true if He created new souls every day. Therefore all souls were created at the same time.
Objection 2. Further, spiritual substances before all others belong to the perfection of the universe. If therefore souls were created with the bodies, every day innumerable spiritual substances would be added to the perfection of the universe: consequently at the beginning the universe would have been imperfect. This is contrary to Genesis 2:2, where it is said that "God ended" all "His work."
Objection 3. Further, the end of a thing corresponds to its beginning. But the intellectual soul remains, when the body perishes. Therefore it began to exist before the body.
On the contrary, It is said (De Eccl. Dogmat. xiv, xviii) that "the soul is created together with the body."
I answer that, Some have maintained that it is accidental to the intellectual soul to be united to the body, asserting that the soul is of the same nature as those spiritual substances which are not united to a body. These, therefore, stated that the souls of men were created together with the angels at the beginning. But this statement is false.
Firstly, in the very principle on which it is based. For if it were accidental to the soul to be united to the body, it would follow that man who results from this union is a being by accident; or that the soul is a man, which is false, as proved above (Question 75, Article 4). Moreover, that the human soul is not of the same nature as the angels, is proved from the different mode of understanding, as shown above (55, 2; 85, 1): for man understands through receiving from the senses, and turning to phantasms, as stated above (84, 6,7; 85, 1). For this reason the soul needs to be united to the body, which is necessary to it for the operation of the sensitive part: whereas this cannot be said of an angel.
Secondly, this statement can be proved to be false in itself. For if it is natural to the soul to be united to the body, it is unnatural to it to be without a body, and as long as it is without a body it is deprived of its natural perfection. Now it was not fitting that God should begin His work with things imperfect and unnatural, for He did not make man without a hand or a foot, which are natural parts of a man. Much less, therefore, did He make the soul without a body.
But if someone say that it is not natural to the soul to be united to the body, he must give the reason why it is united to a body. And the reason must be either because the soul so willed, or for some other reason. If because the soul willed it--this seems incongruous.
First, because it would be unreasonable of the soul to wish to be united to the body, if it did not need the body: for if it did need it, it would be natural for it to be united to it, since "nature does not fail in what is necessary."
Secondly, because there would be no reason why, having been created from the beginning of the world, the soul should, after such a long time, come to wish to be united to the body. For a spiritual substance is above time, and superior to the heavenly revolutions.
Thirdly, because it would seem that this body was united to this soul by chance: since for this union to take place two wills would have to concur--to wit, that of the incoming soul, and that of the begetter. If, however, this union be neither voluntary nor natural on the part of the soul, then it must be the result of some violent cause, and to the soul would have something of a penal and afflicting nature. This is in keeping with the opinion of Origen, who held that souls were embodies in punishment of sin. Since, therefore, all these opinions are unreasonable, we must simply confess that souls were not created before bodies, but are created at the same time as they are infused into them.
Reply to Objection 1. God is said to have rested on the seventh day, not from all work, since we read (John 5:17): "My Father worketh until now"; but from the creation of any new genera and species, which may not have already existed in the first works. For in this sense, the souls which are created now, existed already, as to the likeness of the species, in the first works, which included the creation of Adam's soul.
Reply to Objection 2. Something can be added every day to the perfection of the universe, as to the number of individuals, but not as to the number of species.
Reply to Objection 3. That the soul remains without the body is due to the corruption of the body, which was a result of sin. Consequently it was not fitting that God should make the soul without the body from the beginning: for as it is written (Wisdom 1:13-16): "God made not death... but the wicked with works and words have called it to them."
Source: Summa Theologica (New Advent)