On Monday, organisers and the bands said they had reached an "amicable agreement" over the acts' fees, which were never paid.
The two bands had been in dispute with the Danish festival's organisers after they withdrew when nine young men were trampled to death on 30 June during a performance by US rock act Pearl Jam.
Both bands said it would be "disrespectful" to the families of the dead to continue, a decision attacked by the festival's organisers.
Pet Shop Boys singer Neil Tennant later said the way the organisers handled the tragedy was "unbelievably insensitive" .
On Monday, organisers and the bands said they had reached an "amicable agreement" over the acts' fees, which were never paid.
A joint statement also said: "The Roskilde Festival respects the groups' reasons for not performing after the tragedy.
"All parties hope that lessons learned from the festival will lead to improved safety for all future festival audiences throughout the world."
The deal means organisers will keep some of the money to improve safety at the festival site, 25 miles west of Copenhagen.
The bands' expenses will also be paid, and the remainder will be split between five charities: War Child, which aims to help children caught up in conflicts; anti-censorship organisation Freemuse; Human Rights Watch; SOS Children's Village, which provides homes for children worldwide; and the United Nations' Hunger Site internet initiative.
The sums involved were not released.
A police inquiry found that safety precautions at the festival had been sufficient on the day of the tragedy, the first major accident at the festival since it began in 1971.
Last month, festival organisers unveiled plans for the 2001 event, and promised the stage areas would be improved along with facilities for communication between staff.
A memorial grove of nine trees will also be planted on the site.