Hamid Karzai, who stepped down as president yesterday, refused to sign the deal in a disagreement that symbolised the breakdown of Afghan-US relations after the optimism of 2001 when the Taliban were ousted from power.
"The BSA (bilateral security agreement) will be signed tomorrow, not by the president but by a senior minister," Daoud Sultanzoy, a senior aide of Ghani's, told AFP.
"The signing sends the message that President Ghani fulfils his commitments. He promised it would be signed the day after inauguration, and it will be.
State Department spokeswoman Jen Psaki confirmed that the two countries had agreed to sign the deal today.
US Ambassador James Cunningham will be "signing on behalf of the United States," she said.
"This will enable Afghanistan, the United States and the international community to maintain the partnership we've established to ensure Afghanistan maintains and extends the gains of the past decade," Psaki told reporters.
The BSA will be signed in parallel with a similar agreement between Afghanistan and NATO.
After NATO's combat mission ends in December, the new mission - named Resolute Support - will focus on training and support for the Afghan army and police as they take on the Taliban insurgents.
Negotiations over the pact saw Karzai at his most unpredictable as he added new demands, shifted positions and infuriated the United States, Afghanistan's biggest donor.
He eventually refused to sign the agreement despite a "loya jirga" grand assembly that he convened voting for him to do so, and widespread public support for US troops to stay.
Washington had threatened to pull all US forces out by the end of the year, but it choose to wait through a long election deadlock until Afghanistan finally got a new president yesterday.
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