The final vote count is also scheduled for release, after being delayed for last-minute talks to break a deadlock that plunged Afghanistan into crisis as US-led troops end their 13-year war against the Taliban.
Ashraf Ghani - who won June's run-off presidential vote, according to preliminary results - will become president, with Abdullah Abdullah nominating the person to fill a new post of "chief executive officer" (CEO), which will be similar to prime minister.
Both Ghani and Abdullah claimed to have won the fraud-tainted election. 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 two candidates signed the agreement at a ceremony inside the presidential palace, before they embraced each other and outgoing President Hamid Karzai began a speech. Under the 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 told AFP the official result would be released later today, after the deal was signed.
The future of Afghanistan's relationship with the 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 yesterday.