The exact details of his capture are actually pretty ironic. He was captured due to attempting to hide himself from authorities even further. As stated in Rainbow Six by Tom Clancy:

"And so he'd ended up in Sudan, where he'd decided to take his situation a little more seriously. Some cosmetic surgery had been in order, and so he'd gone to a trusted physician for the surgery, submitted to the general anesthesia-

-and awakened aboard a French business jet, strapped down to a stretcher, with a Frenchman saying, "Bonjour, Monsieur Chacal," with the beaming smile of a hunter who'd just captured the most dangerous of tigers with a loop of string."