The move means that Ahmad Zia Massood, the current vice president, has been taken off his ticket.
Despite dozens of Afghan politicians and leaders showing interest in running, no candidates who would strongly challenge Karzai have registered to run.
Gul Agha Sherzai, a popular governor, withdrew from the race on Saturday, and Fahim was a prominent member of the opposition before agreeing to stand as Karzai's running mate.
Karzai, who has led Afghanistan since the US-led invasion to rem,ove the Taliban from power in 2001, has come under increasing criticism for failing to tackle opposition fighters linked to the Taliban, al-Qaeda and tribal leaders.
He has also been under pressure as civilian deaths in the US-led war continue to rise.