Cardinal Theodore McCarrick of Washington read the letters aloud during Kennedy's burial service at Arlington National Cemetery, The Boston Globe reported Wednesday.
Kennedy's letter, dated July, was delivered to the pope by President Barack Obama, which means Benedict almost certainly read it. The response from the Vatican secretariat is unsigned, customary for papal correspondence.
The senator acknowledged sins and said he had tried, in his public life, to work for the social goals of the church. He asked for the pope's prayers and offered his own.
The response said the pope wanted to express his "concern and his spiritual closeness" to Kennedy.
"The Vatican's warm reply to the senator's letter was in striking contrast to the harshly negative rhetoric some of his critics have directed at him, even in death," said the Rev. Richard McBrien of Notre Dame University.