"The Holy Father did not intend to perform any exorcism," Vatican spokesman Federico Lombardi said in a statement, after the claims by TV 2000, which is owned by the Italian bishops' conference.
"As he often does with sick and suffering people who are presented to him, he simply intended to pray for the suffering person," Lombardi said.
The channel quoted exorcists saying there was "no doubt the pope was either reciting a prayer for freeing from the devil or performing an exorcism."
The footage recorded by Vatican television shows the pontiff briefly laying both hands on the boy's head on the sidelines of a Pentecost ceremony on Sunday.
The boy is seen shaking opening his mouth as if screaming for a few seconds.
TV 2000 director Dino Boffo issued an apology on Tuesday, saying "I unconsciously gave the go ahead for the publication of a piece of news that was true but only partly so, because the Pope denies having performed an exorcism."
The Vatican's former chief exorcist Gabriele Amorth said Sunday that Francis' act "was an exorcism alright and if Father Lombardi denies this, he clearly does not have a clue."
"That was a real exorcism and what is more, the boy the pope exorcised came to me today," Amorth said in a radio interview quoted in La Stampa daily's Vatican Insider insert.
"His name is Angelo and he is possessed by four demons. I performed a long exorcism on him," he added.
Amorth insisted that the pope's gesture "does qualify as an exorcism because an exorcism is also performed by placing one's hands on a person's head and praying, without resorting to written exorcisms."
TV2000, which has previously aired claims that the pope's predecessors John Paul II and Benedict XVI also exorcised the devil, is to broadcast a special programme on Friday devoted to "the pope's struggle against the devil and his seductions".
Exorcism is an ancient practice of driving out demons from a person or place, and exists in several religions including in Roman Catholicism, where it is treated with huge scepticism by many believers.