Some have asserted that the Catholic Church and St. Thomas Aquinas have taught that the substances of bread and wine are annihilated at the consecration. But this can’t be the case because grace does not destroy nature. St. Thomas breaks it down in ST IIIa, q. 75, a. 3:
On the contrary, Augustine says: “God is not the cause of tending to nothing.” But this sacrament is wrought by Divine power. Therefore, in this sacrament the substance of the bread or wine is not annihilated.
Because the substance of the bread and wine does not remain in this sacrament, some, deeming that it is impossible for the substance of the bread and wine to be changed into Christ’s flesh and blood, have maintained that by the consecration, the substance of the bread and wine is either dissolved into the original matter, or that it is annihilated.
Now the original matter into which mixed bodies can be dissolved is the four elements. For dissolution cannot be made into primary matter, so that a subject can exist without a form, since matter cannot exist without a form. But since after the consecration nothing remains under the sacramental species except the body and the blood of Christ, it will be necessary to say that the elements into which the substance of the bread and wine is dissolved, depart from thence by local motion, which would be perceived by the senses. In like manner also the substance of the bread or wine remains until the last instant of the consecration; but in the last instant of the consecration there is already present there the substance of the body or blood of Christ, just as the form is already present in the last instant of generation. Hence no instant can be assigned in which the original matter can be there. For it cannot be said that the substance of the bread or wine is dissolved gradually into the original matter, or that it successively quits the species, for if this began to be done in the last instant of its consecration, then at the one time under part of the host there would be the body of Christ together with the substance of bread, which is contrary to what has been said above. But if this begin to come to pass before the consecration, there will then be a time in which under one part of the host there will be neither the substance of bread nor the body of Christ, which is not fitting. They seem indeed to have taken this into careful consideration, wherefore they formulated their proposition with an alternative viz. that (the substance) may be annihilated. But even this cannot stand, because no way can be assigned whereby Christ’s true body can begin to be in this sacrament, except by the change of the substance of bread into it, which change is excluded the moment we admit either annihilation of the substance of the bread, or dissolution into the original matter. Likewise no cause can be assigned for such dissolution or annihilation, since the effect of the sacrament is signified by the form: “This is My body.” Hence it is clear that the aforesaid opinion is false.
To sum up, if the substances of bread and wine were destroyed and annihilated, transubstantiation would not render a miraculous transformation but a miraculous replacement.