The partial agreement was the result of 18 months of work in which 3,000 victims of the rebels, government troops and right-wing paramilitary groups participated and offered thousands of proposals. Sixty victims gave testimony to peace negotiators in Havana, site of the peace talks for the past three years.
The accord creates a truth commission to clarify what happened in the war and promises to search for thousands of missing people, identify their remains and return them. It also attempts to ensure those affected will not be victimized again.
"The justice agreement was the most complex, the most difficult. It's a very important step to be able to end the conflict soon," Santos said.
While attempting to offer as much amnesty as possible, the courts would reduce sentences for those who admit guilt and exclude from amnesty those responsible for war crimes or crimes against humanity.
Former rebels and soldiers who confess to crimes committed during the conflict will receive 5-year to 8-year sentences of supervised "restrictions of liberty," which would involve surveillance and monitoring but not jail.
"Let's be clear: We've always said there wouldn't be prison in these cases," said Humberto de la Calle, the government's chief negotiator.
Lead rebel negotiator Ivan Márquez said it was the first agreement in Colombia to forgo a general amnesty and instead "reveal all the violations of rights and all those responsible."
Doubts over the terms of punishment have caused consternation in Colombia, where some are unwilling to forgive the crimes of their former enemies. Other critics complain FARC members might escape punishment or extradition to the United States, where some are wanted on drug-trafficking charges.
Any final, comprehensive peace deal would need to be approved by Colombian voters.