Rebel leader Riek Machar was among those granted a pardon by Kiir.
Those who “waged war against in the government” were granted general amnesty, Kiir stated late Wednesday.
The president also reiterated a call for his forces to observe a ceasefire agreed in June by both the government and Machar’s rebels.
The decision came days after the warring parties struck a power-sharing agreement to end the civil war, which has killed tens of thousands of people and displaced millions.
The deal gives the parties eight months to form a transitional government. The agreement was one of many signed over the past few years that have failed.
South Sudan’s war began after Kiir accused his then-vice president Machar of plotting a coup against him in 2013.
Sunday’s power-sharing agreement paves the way for Machar to return to South Sudan as one of five vice-presidents under Kiir.
A final peace accord must now be signed – under the auspices of regional bloc, the Intergovernmental Authority on Development – followed by the formation of a transitional government that will hold power for three years until elections can be organised.