A three judge bench by majority of 2:1 held the crime committed by convict Manoharan as "rarest of rare" category and ruled he did not deserve any sympathy.
The majority judgement also said that it was unlikely that the convict, if set free, would refrain from committing such crime yet again.
Justices R.F. Nariman and Surya Kant upheld the death penalty while Justice Sanjiv Khanna stressed on life imprisonment.
Justices Nariman and Kant found that the offence committed by the convict was so grave that it has shaken the conscience of this court and of society.
The court turned down the convict's plea seeking leniency citing young age and said that such convict poses a continuous burden on the state and risk to society, hence warranting more serious intervention by the courts.
On August 1, the Supreme Court had upheld Madras High Court and a trial court order that had awarded the death penalty to Manoharan, saying that the offence fell under the "rarest of rare" category.
Thereafter Manoharan moved court seeking review of the death sentence.
On October 29, 2010, Manoharan and co-accused Mohanakrishnan had picked up the girl and her seven-year-old brother from outside a temple when they were preparing to go to school.
They had brutally gang-raped the girl and tried to kill the minors sibling by poisoning. After they did not die, they threw the minors into a canal where they drowned.
Mohanakrishnan was later shot dead in an encounter.
"It was not in the spur of the moment or a crime of passion, but craftily planned, meticulously executed with multiple opportunities to cease and desist," Justices Nariman and Kant said.
"We are also not inclined to give leeway of the lack of criminal record, considering that the current crime was not just one offence, but comprised of multiple offences over the series of many hours."
The court in its order noted that the convict was remorseless.
"There is nothing to support the characterisation of the accused as being a helpless, illiterate young adult who is a victim of his socio-economic circumstances," the court said.
( With inputs from IANS )