Khan's mysterious death in July 2012 came one day after he collected more than $400,000 from a million dollar lottery jackpot.
"The body was in a state of advanced decomposition. We were able to identify the major organs and take samples of each of those for toxicological analysis," Cook County Medical Examiner Dr. Stephen Cina said.
The final results of the autopsy could determine how cyanide entered Khan's body and will be ready in a few weeks, according to Cina.
Khan, who was buried six months ago, was pulled from the ground around 8:00 a.m. and placed inside a green tent.
About an hour later, his body was removed from the tent and placed in a hearse.
An imam, a Muslim religious leader, was present to ensure the work was carried out in accordance with Khan's faith.
Onlookers were kept at a distance at the exhumation.
The hearse then went to the medical examiner's office where the two-hour autopsy was conducted.
"We took samples of most of the solid organs, hair and finger nails. We also took some samples of dirt from the gravesite as well," Cina said.
The 46-year-old West Rogers Park man was initially found to have died of natural causes. But after a relative requested further testing, the medical examiner determined the death was a homicide and Khan died from cyanide poisoning.
"Cyanide over the post-mortem period actually can essentially evaporate and leave the tissues, so it is possible that cyanide that was in the tissues is no longer in the tissues after several months. We'll just have to see how the results play out," Cina said.
No one has been charged in Khan's death including his widow, who prepared his final meal and has maintained her innocence.
"We were able to recover some stomach contents and they'll be tested," Cina said.
Khan's brother, Imtiaz Khan, said the family has faith in U.S. authorities.
"This is a great country. I have full confidence that the truth will come out and they will find out how, when, when did it happen, how it happened. It will come out," Imtiaz Khan said.
Khan's widow, Shabana Ansari, told ABC7 News last week she supports the exhumation because "God is going to reveal the truth."
Khan's siblings, along with his teenage daughter from a previous marriage, are in a legal battle with his widow and also say they want justice served.
"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 Minhaj Khan, nephew.