A team of forensic experts from Delhi and Hyderabad conducted the autopsy on the skeletal remains at the graveyard in Tenali town of Guntur district of Andhra Pradesh.
The body was exhumed early Tuesday in the presence of some Muslim religious leaders and under the supervision of a CBI official leading the probe into the sensational case, which saw many twists and turns.
The forensic experts collected samples and sealed them into boxes for detailed examination.
The federal agency, which began the investigation last year on the direction of the High Court, hopes to gather some clues in the horrific crime, which had shocked then undivided Andhra Pradesh.
Blood-stained body of the 19-year-old was found with multiple stab injuries in the bathroom of a private women's hostel in Ibrahimpatnam near Vijayawada on the night of December 27, 2007.
The victim's family had alleged that the evidence was wiped out from the scene of the offence to shield the guilty. It claimed that a relative of the then minister and his friends were involved in the crime, but innocents were arrested and sentenced.
In 2008, police had claimed that one Satyam Babu, arrested in a cell phone robbery case, confessed to Ayesha's murder.
The Mahila Court in Vijayawada, on September 10, 2010, convicted and sentenced Satyam Babu to life imprisonment.
In 2017, the Hyderabad High Court acquitted Satyam Babu, a Dalit youth. It also ordered action against the police team that investigated the case.
Subsequently, the state government constituted Special Investigation Team (SIT) to conduct a fresh probe. The High Court was supervising the probe by SIT, which found that all records relating to the case were destroyed by the trial court.
Expressing its unhappiness over the manner in which SIT conducted the probe, the court in November 2018 handed over the case to CBI.
The agency was also directed to probe the destruction of records relating to the case. The CBI booked a case against some employees of the trial court.
Meanwhile, victim's mother has appealed to Chief Minister Y.S. Jagan Mohan Reddy to ensure that it becomes the first case to be tried under Andhra Pradesh Disha Act.
The State Assembly on Friday passed a Bill, providing for death penalty to rapists. It also fixed 21 days as the period to complete the investigation and trial.
The victim's mother told media persons on Saturday that over the last 12 years, they lost confidence in police and the entire system due to the manner in which the case was handled by them. She supported police action of killing four accused in gang-rape and murder of a veterinarian in Hyderabad early this month, and asked why similar action is not taken in other cases to ensure speedy justice.
"Justice is delivered in select cases. It is only for the rich and powerful while victims from ordinary and poor families like us are made to run from pillar to post," she said.
The Disha Act is named after the victim of Hyderabad case while Nirbhaya Act was passed after the gang-rape and murder of a girl in Delhi in 2012.
( With inputs from IANS )