The girl, fondly called as Chinnari, was playing with her elder sister when she accidentally fell in the nearly 450-feet-deep open borewell in a field at Ekkareddyguda village of Chevella mandal, about 60 kms from Hyderabad, on Thursday around 7.15 pm.
"She is declared dead...we called off the rescue operation at 6 am after the remains were retrieved," Cyberabad Police Commissioner Sandeep Shandilya told PTI.
The authorities had yesterday said chances of the toddler's survival were bleak.
The efforts to rescue the child had started from 8 pm on Thursday using different methods. However, today her remains were found stuck at around 245 feet, police said.
"After the postmortem was conducted, the child's remains were handed over to her family members and taken to her native Gorepally village," Chevella police station's sub-inspector N Sridhar Reddy said.
After the girl fell into the borewell, a parallel trench was dug along the hole with the help of earth excavating machines even as the rocky area and rains had hampered the rescue work.
Apart from police, the fire department, National Disaster Response Force (NDRF) personnel and a team of Oil and Natural Gas Corporation (ONGC) officials were also involved in the rescue operation along with a team of doctors.
The Cyberabad police had on Friday registered a case against the land owner, Malla Reddy, under IPC section 336 (act endangering life or personal safety of others).
In October 2014, a four-year-old girl died after falling into a nearly 300-feet-deep borewell in Ranga Reddy's Manchal village.
Get the latest election news, live updates and election schedule for Lok Sabha Elections 2019 on ndtv.com/elections. Like us on Facebook or follow us on Twitter and Instagram for updates from each of the 543 parliamentary seats for the 2019 Indian general elections.