The girl, daughter of a labourer, had gone to a shop at a short distance from her house in Bhikampur locality on Tuesday but did not return home, police said.
As her family launched a search, they recovered the mutilated body of the girl who also appeared to have been sexually assaulted, police said.
A manhunt was launched for the accused and police zeroed in on one Arvind, 32, a former employee of the shop where the girl had gone.
The accused, who had lured the child with sweets, was found lying on the roadside in an inebriated state.
As he was being brought to the police station, a group of locals attacked him, police said.
He was admitted to the Jawaharlal Nehru Medical College Hospital with multiple injuries, where he succumbed on Wednesday night.
A case of murder has been lodged against 200 unnamed persons in this connection, police added.