It is the third and final amnesty decree signed by Mr Santos.
More than 7,000 rebels in total have been granted amnesty or released from prison as part of their reintegration into Colombian society.
Last month the Farc completed its disarmament process.
The rebels handed all its 7,000 registered weapons to the United Nations mission in Colombia.
Earlier on Monday, the United Nations Security Council voted to set up a new mission in the country, which from September will oversee the implementation of the peace deal.
The move puts an end to more than five decades of conflict.
The Marxist rebel group was found in 1964 to defend the rights of landless peasants.
It entered formal peace negotiations with the government in 2012. The talks were held in Cuba and lasted four years.
The final agreement was rejected by the Colombian people in a referendum last October. But a reviewed version was approved by Congress a month later and signed into law.
The Farc has agreed to give up its armed struggle to become a political party.
A key part of the agreement was the rebels’ reintegration to civilian life. It was agreed that all Farc members who did not commit serious crimes would be granted amnesty.
The three decrees signed by Mr Santos have benefited 6,005 former rebels. Another 1,400 who were serving prison sentences have been released in the past few months.
Mr Santos won last year’s Nobel Peace Prize for his peace efforts.
Following the success of the Farc negotiations, Colombia’s second rebel group, the National Liberation Army, or ELN, also entered formal peace talks. They are being held in neighbouring Ecuador.
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