"I am deeply sorry for the pain and suffering the victims have endured and I assure them as their pastor that I too share in their suffering," Benedict said during an address at a Mass at the church's World Youth Day in Sydney.
"Those responsible for these evils must be brought to justice," he said.
The pope said the scandal had badly damaged the church.
"These misdeeds, which constitute so grave a betrayal of trust, deserve unequivocal condemnation," he said. "They have caused great pain, they have damaged the church's witness."
Anthony Foster, the father of two Australian girls who were allegedly raped by a Catholic priest, said he was disappointed that the apology repeated the church's expressions of regret but offered no practical assistance for victims.
"What we haven't had is an unequivocal, unlimited practical response that provides for all the victims for their lifetime," he said. "The practical response needs to include both financial help ... and psychological help."
Support groups for victims of church abuse in Australia, whose numbers are not known but who activists say are in the thousands, say the church covered up of the scale of the problem and fought compensation claims lodged in civil courts.
"Sorry is not enough. Victims want action, not just words," the Broken Rites group said in a post on its Web site.
"It is just a drop in a bucket - a bucket full of tears that all of us who work with victims have been sitting with for 25 to 30 years in Australia," said Helen Last from the victims' group In Good Faith and Associates.
Benedict has expressed regret before about the clergy abuse scandal that has rocked the church in recent years
- notably during a visit to the United States in April when he also met privately with a small number of victims.
But the language of Saturday's apology was stronger than the pope's comments in the United States.
Vatican spokesman Rev. Federico Lombardi said the pope added the words that he was deeply sorry to the original text given to reporters because he wanted to "personally underline" that he felt close to the victims.
There was no immediate word whether Benedict would meet with victims during his Australia trip, which ends Monday. Foster has said he wants a meeting with the pontiff during the trip.
The pontiff is in Australia to lead hundreds of thousands of pilgrims in World Youth Day, a global celebration meant to inspire a new generation of Catholics. They welcomed the apology.
"I think it's a good gesture, but the person who is responsible for these actions should be made responsible," said Daniel Bidinger, 25, of Germany. "The church should be open about it and shouldn't cover up these incidents."