Hardy's novel reads a bit like an epic, but it's still possible to shoehorn it into a traditional three act plot structure if you're willing to push through a really long Act 2. As with most things in Jude the Obscure, the act breaks are all about Christminster.
Let's take a look at how it all shakes out in three acts:
Act 1 lines up perfectly with Hardy's "Part First: At Marygreen". This covers Jude's childhood, his commitment to self-education, his meeting of and marriage to and separation from Arabella. The act comes to a close with Arabella going on her way to Australia and Jude re-committing to his Christminster dream:
"He would go to Christminster as soon as the term of his apprenticeship expired" (1.11.42).
Okay, to make this structure work, Act 2 has to cover most of the novel. It starts with Hardy's "Part Second: At Christminster" and doesn't close until right before Hardy's "Part Sixth: At Christminster Again." (Told you it was all about Christminster.)
This Act covers almost all of the pursuing, missed opportunities, and ups and downs of Jude and Sue's relationship. There are marriages, divorces, births, and a whole lot more. This Act dominates the novel, which makes it clear that despite the Christminster dream, this is really a tragic love story, and not only a story about the failure of a man who wants to be a scholar.
That leaves "Part Sixth: At Christminster Again" to serve as Act 3. Jude brings Sue and the children back to the city of his dreams despite Sue's deep desire to stay away from Christminster. This return proves to be his undoing.
Little Father Time kills the babies and himself, Sue remarries Phillotson, Jude remarries Arabella, Jude and Sue have their final scene in which they profess their love for each other, and then Jude dies. Yep, this Act is not a happy one—not that any of the others have been precisely happy. But this one is clearly the worst.