"The deadline for him is September 1," said Nigerian Ambassador Joy Ogwu, who chairs the council this month.
"He has room to play," she told reporters.
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"The current peace we are signing today has so many things we have to reject," Kiir said at the ceremony attended by leaders from Kenya, Ethiopia and Uganda.
"Such reservations, if ignored, would not be in the interests of just and lasting peace," he said.
The 15-member council had threatened on the eve of the signing to take "immediate action" if Kiir failed to sign, or signed with reservations.
But the Nigerian envoy made clear that the council would not move until Tuesday.
"He has until September 1," said Ogwu. "We'll wait."
Rebel leader Reik Machar already signed the deal on August 17, but at the time, Kiir only initialed part of the text and was given until September 1 to return to the table to fully accept the accord.
The United States has circulated a draft resolution that would impose an arms embargo and targeted sanctions on those who undermine peace efforts in South Sudan.
South Sudan's civil war erupted in December 2013 when Kiir accused his former deputy Machar of planning a coup, unleashing a wave of killings that has split the country along ethnic lines.
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