The 42-year-old rapper was just 11 when Adnis Reeves descended into alcoholism and left their home in New York and the `99 Problems` hitmaker - whose real name is Shawn Carter - was left devastated by the departure of his "superhero".
He said: "If your dad died before you were born, yeah, it hurts, but it`s not like you had a connection with something that was real. Not to say it`s any better, but to have that connection and then have it ripped away was, like, the worst. My dad was such a good dad that when he left, he left a huge scar. He was my superhero."
The pair didn`t reunite until 2003 - despite attempts by Jay`s mother Gloria Carter to arrange meetings - and while the music mogul said there was "no excuse" for his dad`s conduct, he forgave his absent parent, who died just a month after they held clear-the-air talks.
Speaking to the forthcoming Men of the Year issue of America`s GQ magazine - who named him King of the Year - Jay said: "[I talked about] what it did to me, what it meant, asked him why. There was no real answer. There was nothing he could say, because there`s no excuse for that. There really isn`t.
"So there was nothing he could say to satisfy me, except to hear me out. And it was up to me to forgive and let it go."
The rapper`s wife Beyonce Knowles is currently expecting the couple`s first child and Jay has pledged to be a hands-on dad as he knows material possessions are not as important as being there for his offspring.
He said: "Providing - that`s not love. Being there - that`s more important. I mean, we see that. We see that with all these rich socialites. They`re crying out for attention; they`re hurting for love.
"I`m not being judgmental - I`m just making an observation. They`re crying out for the love that maybe they didn`t get at home, and they got everything. All the material things that they need and want. So we know that`s not the key."
Asked if he plans to change diapers, he added: "Of course. 100 per cent."
Also celebrated in GQ`s Men of the Year issue are Justin Timberlake, Jimmy Fallon, Michael Fassbender and Mila Kunis.