The final vote count is also scheduled for release, after being delayed for last-minute talks to break a deadlock that has plunged Afghanistan into crisis as US-led troops end their 13-year war against the Taliban.
Ashraf Ghani - who won June's run-off vote according to preliminary results - is set to become President with Abdullah Abdullah nominating his pick for the new post of "chief executive officer" (CEO), which will be similar to the PM.
Both Ghani and Abdullah claim to have won the fraud-tainted election, and the United Nations has pushed hard for a "national unity government" to avoid a return to the ethnic divisions of the 1990s civil war.
"The presidential candidates... will sign an agreement on the structure of a national unity government today (Sunday) at 12.00 pm (1300 IST)," Aimal Faizi, spokesman for outgoing President Hamid Karzai, said via Twitter.
Under the Afghan constitution, the President wields almost total control, and the new government structure will face a major test as the country's security and economic outlook worsens.
The vote count has been plagued by months of setbacks amid allegations of massive fraud, emboldening the Taliban insurgents and further weakening the aid-dependent economy.
Independent Election Commission officials said that the official result would be released later on Sunday after the deal was signed.
The future of Afghanistan's relationship with US-led NATO alliance also hangs in the balance after Karzai refused to sign a security pact to ensure a continued foreign military presence after this year.
NATO's top military commander said a unity government would enable the rapid conclusion of the pact.
"We are hoping for very fast signatures. And that would be important because it brings great stability to the conversation of our continued support," US General Philip Breedlove said on Sunday.
A ruling coalition between the opposing camps is likely to be uneasy after a bitter election that has revived some of the ethnic loyalties of the civil war that led to the Taliban taking power in Kabul in the 1990s.
The new administration will have to stabilise the economy as international aid falls, and deal with worsening unrest nationwide.

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