The audit was agreed to last month, and will determine which candidate from the June 14 run-off election succeeds President Hamid Karzai. Preliminary election results showed former Finance Minister Ashraf Ghani in the lead with 56.44 percent of the vote, and former Foreign Minister Abdullah Abdullah trailing behind with 43.56 percent.
U.S. Secretary of State John Kerry championed the audit during a visit to Kabul last month. Both candidates accepted the terms of the process at the time.
The audit was temporarily suspended amid concerns by both camps of electoral fraud and the process of discounting suspicious ballots. Abdullah's camp held out Sunday and threatened to boycott the audit.
At 2 p.m. local time on Sunday, Afghanistan's Independent Electoral Commission announced that the audit would resume without Abdullah's participation, adding that "the door ... is open to them."
Around 7 p.m., United Nations officials announced that Abdullah's camp had decided to support the audit once the U.N. had provided clarification on certain aspects of the audit and agreed to necessary changes in the process of invalidating ballots.