Though the BBC claims that he died of pancreatic cancer, we won't know until the biography hits. I believe his cancer went into remission, and metastasized in his liver, forcing a liver transplant, but the process of metastasis continued until it killed him.
Jobs rejected invasive treatment initially, but he had the tumor removed. Of course, surgery leaves some cancerous around, and Jobs did not have chemotherapy to kill the remaining cells, so perhaps they remained around, growing, growing, growing...
I am not a doctor, but I believe that metastasis of cancer cells throughout his body killed him. That, or liver failure because of organ rejection.