The child, Fatehveer Singh, was brought to the PGI hospital in Chandigarh, some 130 km from the accident spot, soon after he was retrieved from the well, officials said.
However, there is no official confirmation from doctors about the health of the child.
Chief Minister Amarinder Singh expressed grief over his death.
"Very sad to hear about the tragic death of young Fatehveer. I pray that Waheguru grants his family the strength to bear this huge loss," he said in a tweet.
"Have sought reports from all DCs (Deputy Commissioners) regarding any open bore well so that such terrible accidents can be prevented in the future," he added.
As he was retrieved, the child's grandfather Rohi Singh told the media on the spot: "Why was he taken to the hospital when he is no more."
He claimed that the body of the child had grievous wounds. "He was pulled out (of the borewell) by using strings."
A health worker in the PGI's emergency ward told reporters the child's body was badly decomposed and smelly.
"It seems the child died two days ago," he added.
The boy, who had been trapped in the abandoned borewell since June 6, was retrieved by the rescuers of the National Disaster Response Force (NDRF).
Sangrur Deputy Commissioner Ghanshyam Thori said it was one of the toughest operations carried out by the NDRF.
Lack of expertise and technical snags one after another were blamed for the delay in the massive rescue operation.
Special teams had been working day and night in a tunnel that was dug parallel to the abandoned borewell.
Meanwhile, tension prevailed among villagers in Sangrur over the inability of the state government to timely retrieve the toddler.
Thousands of angry protesters blocked the road leading to Bhagwanpura village in Sunam sub-division, some 15 km from district headquarters at Sangrur, where the incident occurred.
On March 22, a one-and-a-half-year-old boy, who fell into a 70-foot narrow borewell in Haryana's Hisar district, was rescued after a 48-hour operation.
In July, 2006, Army engineers in Haryana's Kurukshetra town had rescued a little boy trapped in a 60-foot well for two days.
( With inputs from IANS )