The irony of the slave and his master's daughter
Instead of hating his master, Jacob learns that even his slave master is a real human, and so when he meets the slave master's daughter, he falls in love with her. He doesn't have enough hatred to keep him from taking her as his wife. This ironic open-mindedness defines Jacob throughout the novel.
The irony of a second life
When someone loses their family, the first response is usually a season of mourning. Many never recover from the grief, and of those who do, many never move on to another relationship, so the fact that this story is about Jacob's second family, after losing his first family in an ethnic massacre, is ironic. It's ironic that in the aftermath of his family's death, he falls in love and finds a new family to love.
The irony of hatred and death
For a community that has been so harmed by racism and bigotry, Jacob's community is pretty racist and bigoted. The irony here is that instead of discovering that humans are equal by nature, and that diversity exists as a thing of beauty to be treasured, the members of Jacob's community decide to be closed off and hateful toward foreigners. Their mistreatment of Sarah's bones after her death is punished when they die and are buried right beside her. In other words, death is not a respecter of human hatred. Death treats all men the same, regardless of what they think about themselves or others.
The irony of religious experience
To the reader, the novel's events probably seem normal and straightforward, but the implication from Jacob's deep religious beliefs is that no matter how normal his life events may seem on the surface, Jacob's experience of life is deeply mysterious and religious, from the first page to the last. Look for instance at the death of his wife in childbirth. Instead of taking that the way most men would take it, with hatred toward fate and toward God, Jacob realizes that the child must be like Benjamin, whose mother died in childbirth too. What would be normal events to others are supernatural signs and omens to Jacob.
The irony of Jerusalem
By returning his family to Jerusalem, Jacob literally completes the Jewish story for his own family, returning his Jewish family to their Jewish holy lands. Plus, just like Jacob interprets seemingly regular life events through the lens of religious experience, he also views Jerusalem as a truly spiritual city. To the Jews, Jerusalem is like the port city between heaven and earth. For Jacob to raise his son in Jerusalem is another sign of his commitment to his Jewish tradition. But his love for his wife shows that Jacob did not fall into the trap of religious hypocrisy, like his community in Poland did.