Wednesday's announcement came almost a month after eight million Afghans defied threats of violence to vote in the elections.
"Karzai is the winner," the UN-Afghan joint electoral commission's spokesman, Sultan Baheen, said after the findings of a fraud probe concluded that "shortcomings" did not affect the poll's outcome.
The results of the 9 October ballot will be formally certified at a public ceremony in Kabul at 3pm (1030 GMT), United Nations spokesman Manoel de Almeida e Silva said.
But Karzai will not be present for the declaration of his victory, as he has flown to Dubai to attend the funeral of United Arab Emirates President Shaikh Zayid bin Sultan Al Nahyan.
"The president left Kabul for Dubai today to participate in the funeral ceremony of His Majesty Shaikh Zayid," Karzai's campaign spokesman Hamid Elmi said.
"He was a close friend of Afghanistan," Elmi said of Shaikh Zayid.
The drawn-out vote count was completed only last Thursday.
Preliminary results gave Karzai a landslide win of 55.4% with a 39.1 point lead over his nearest rival, former education minister Yunis Qanuni.
"This was a commendable election, particularly given the very challenging circumstances"
Joint Electoral Management Body statement
The favourite of the powerful anti-Taliban Northern Alliance, Qanuni was said to be waiting until the results were publicly certified and may hold a press conference later.
The election commission, known as the Joint Electoral Management Body, had to assess the report of a three-person panel of experts, plus the findings of its own investigation into irregularities, before certifying the election as "free and fair".
The expert panel found the poll's "shortcomings" did not affect the overall result.
"This was a commendable election, particularly given the very challenging circumstances," the panel's report said in the conclusion.
"There were shortcomings, many of which were raised by the candidates themselves," said the panel. "These problems deserve to be considered to ensure the will of the voters was properly reflected, and to help shape improvements for future elections.
"But they could not have materially affected the overall result."
The panel was set up by the UN after 14 of the 18 candidates threatened to boycott the election in the middle of voting on 9 October over alleged irregularities, mainly arising from the failure and mix-up of indelible ink which was meant to stain voters' fingers to prevent repeat voting.
Presidential candidate Yunis
Qanuni is set to concede defeat
Panel member Craig Jenness, a former Canadian diplomat, said Afghans deserved to be proud of their first election.
"The 2004 Afghan presidential election was conducted in a relatively calm and secure environment with high turnout and much enthusiasm and substantial participation of women," he said.
"Many voters made personal sacrifices and braved difficult conditions to cast their ballot on 9 October.
"The Afghan population is justified in the pride it has overwhelmingly expressed in this election."
On the other hand, critics have pointed out that the elections did not meet international standards due to the country's weak electoral system and lack of international monitors.
Moreover, the conclusion of the historic ballot and Karzai's massive victory was overshadowed by the abduction of three UN election workers last week.
Annetta Flanigan from northern Ireland, Shqipe Habibi from Kosovo and Angelito Nayan from the Philippines were kidnapped from their UN-marked vehicle on a busy Kabul road, just as the end of the count was announced.
"How can we say these people are Muslims? How can we accept them?"
Former president Burhan al-Din Rabbani talking about the kidnappers
The abduction has sparked fears among expatriate workers of Iraq-style captures in Kabul and could undermine parliamentary elections scheduled for next April.
The group holding the three UN workers extended a deadline for their threatened execution until Wednesday night, a spokesman said.
"We have extended the deadline because we are hopeful about negotiations," Sayyid Khalid Agha, of the Jaish-e Muslimin (Army of Muslims), told Reuters. He gave no new specific time.
The group had threatened to kill the three hostages unless authorities released all Taliban prisoners in US custody in Afghanistan and Guantanamo Bay by 0730 GMT on Wednesday.
The group's leader, Mullah Sayyid Muhammad Akbar Agha, said on Tuesday that negotiations with a "tajir" - an influential trader with wide contacts - were continuing and while the deadline for the prisoner release remained in place, it could be extended if negotiations progressed.
The government has previously negotiated the release of several foreign nationals kidnapped by Taliban fighters, in return for a ransom, and some security sources say a ransom could be the best hope in this case.
Disquiet has been steadily growing among Afghans over the kidnappings.
Fears of violence at the elections
On Tuesday the head of the country's council of religious elders said it was a sin for Muslims to harm UN workers.
"Islam is a religion of peace and kindness," Shaikh al-Hadith Fazel Hadi Shinwari, head of the All Afghanistan Ulama, said in a statement issued through the Nato-led International Security Assistance Force (ISAF).
"These people have come to serve the people of Afghanistan."
Former president Burhan al-Din Rabbani, still an influential figure, also called the kidnappings un-Islamic.
"How can we say these people are Muslims? How can we accept them?" he said.