"His holiness assured them of his prayers for their intentions, for their families and for all victims of sexual abuse," a Vatican statement said.
The pontiff, on a six-day tour of the US, had not been expected to meet victims of abuse during his visit.
'Symbolic' meeting
During the meeting, he was also given a book in which the names of more than 1,000 victims of abuse by priests were listed.
Gary Bergeron, a victim of abuse from Boston, one of the parishes worst hit by the scandal, called the meeting "a long-sought-for step in the right direction".
"The Catholic Church is partly based on symbolism, and I think the symbolism had he not met with survivors would have been horrendous,'' he told the Associated Press.
But Barbara Blaine, the founder of the Survivors Network of those Abused by Priests, told Al Jazeera that she would like to see action, not just words and gestures.
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"No words of mine can describe the pain and the harm inflicted by the sexual abuse of minors"
Pope Benedict XVI |
Saying that many abusive priests had been given refuge by the church and been able to escape prosecution, she called on the pope to assist in putting such clergy behind bars.
A series of abuse scandals in the US involving the Catholic Church came to light in 2002, sparking legal action that led to more than $2bn being paid out in settlements to victims.
Benedict earlier acknowledged at an open air mass in Washington that the priest sex abuse scandal in the US had sometimes been "very badly handled" by the church.
"No words of mine can describe the pain and the harm inflicted by the sexual abuse of minors," he told the congregation.
"Nor can I adequately describe the damage that has occurred within the community of the church."
However, he also addressed the church's sex abuse problems in the wider context of secularism and the over promotion of sex in the US.
"What does it mean to speak of child protection when pornography and violence can be viewed in so many homes through media widely available today?" he said.