Union Minister Venkaiah Naidu was among those who paid tributes to the 40-year-old, who died while scaling a mountain between Argentina and Chile last month.
"The last rites were performed with state honours in a family field in Gandhijana Sangam in Nellore district," a Government official said.
Mr Naidu said Malli's demise is a big loss to the nation.
People in hundreds came to Gandhijana Sangam from surrounding villages to have a last glimpse of the son-of-the-soil, who figures in world record books for his mountaineering feats.
Malli's body arrived in Delhi from Argentina yesterday and it was later flown to Chennai in an Air India flight. His sister Dorassanamma accompanied the body, a PIB release had said.
Malli, who had set a record of climbing seven summits across the seven continents, including the world's highest peak Mount Everest, left for Argentina towards the end of March and went missing, and was later found dead.
Mr Naidu, who hails from Nellore district, had sought intervention of External Affairs Minister Sushma Swaraj to bring back the mountaineer's body.