First of all, I'm going to clarify your question:
- By "ontological change" I'm going to assume the meaning represented in this blog article about how St. Thomas understood the ontological change happening within the Sacraments of Eucharist, Baptism, Confirmation, and Holy Order. So your question is about whether there is similar ontological change within human nature.
- I'm going to address ontological change within individual believer's human nature, NOT the human nature of all human beings collectively, since God calls a person to his Kingdom one person at a time.
In mainstream Christianity, Catholic, Protestants, and Eastern Orthodox included, when we believe in Christ we will be reborn and a new life starts its existence within us, nurtured by the Holy Spirit. This is the life that produces the fruits of the Holy Spirit. Christianity teaches that the old self and the new self are still contending with each other, but we are supposed to "put on Christ", "crucify our old self" and cooperate with the Holy Spirit in this sanctification/regeneration process so we become more and more purified from the effects of sins in our old life toward conformity with the image of Christ. Therefore the new life becomes stronger and the old life becomes weaker, and just before we enter heaven the process is complete and by this time we become fully Christlike. I believe this is what Aquinas meant by your quote "God himself acts in human nature by regenerating it from within."
While I believe all 3 traditions will agree that there is something NEW added to us (in fact, the Catholic article I quoted above characterized this new life as "ontological change"), whether there is "ontological change" within the fallen human soul after salvation I think it's a matter of debate, since Eastern Orthodox seems to say YES (they understand it as theôsis, a deification process) while Roman Catholic and Protestants seem to say NO.
I came across two blog articles, one from the Western Reformed tradition, another from the Eastern tradition, which describes how the theology of each tradition grapples with the NATURE of the human soul after this new life is added while on the process of becoming like Christ. (I should include one from the Roman Catholic tradition, but I didn't have the time to find one).
Representing the Western (Reformed) tradition is Terrance L. Tiessen emeritus professor of systematic theology writing his deep reflection of Transformation through union with Christ based on a book he is summarizing, Union with Christ: in Scripture, History and Theology, plus 2 papers he read from a recent theological conference. A scholarly peer review of the book is here. All three represent the effort to reevaluate the theologies of the Patristic period and the Eastern Orthodox tradition from the Reformed soteriological perspective (Ordo Salutis) especially how the fear of Greek philosophy led to the neglect of the ontological aspect of salvation within the Reformed tradition.
Representing the Eastern Orthodox tradition is Fr. Stephen Freeman, a priest of the Orthodox Church in America writing a blog article Being Saved - The Ontological Approach where he contrasted the Eastern Orthodox tradition of understanding salvation in ontological terms since the Patristic period with the Western tendency to use moralistic language.
We can see signs of fruitful reassessment of each tradition's theology being more aware of the other, which is a welcome development in Ecumenism by going back to how the early Christians and the Church Fathers understood salvation. While both articles don't answer definitively whether there is ontological change in our human nature when we believe in Christ, I hope those 2 articles can point you in the right direction.