Chief Cook County Medical Examiner Stephen J. Cina told a news conference the body was in an advanced state of decomposition but samples were taken for toxicological analysis, the Chicago Tribune reported.
Khan, 46, died July 20, one day after collecting a $425,000 lottery check. The death initially was ruled as from natural causes but after a relative asked for further investigation, an examination of initial toxicology tests indicated the presence of cyanide.
Cina said Friday's autopsy lasted just a few hours. The body was to be re-interred Monday.
Samples of Khan's lungs, liver and spleen, as well as stomach and intestinal contents, bone, nail and hair were taken, Mary Paleologos, a spokeswoman for the medical examiner's office said.
Investigators said they hope to find more answers on how the cyanide entered Khan's body.
"After he won the lottery and the next day later he passes away, it's very awkward. It raises some eyebrows. When we found out there was cyanide in his blood after the extensive toxicology reports, we had to believe that somebody had to kill him," said Imtiaz Khan, a brother.
Urooj Khan's widow Shabana Ansari, who prepared his last meal, has denied having anything to do with her husband's death and has said she supports the exhumation because "God is going to reveal the truth."
2014: NFL Cheerleaders [PHOTOS]
SUNY Canton cancels classes over threat