Karzai also named candidates for six other vacant positions. He nominated Assadullah Khalid, a former governor of Kandahar province, to be the minister of border and tribal affairs, and Anwarul Haq Ahadi, a former finance minister, to head the ministry of commerce.
The nominations will now go before the Wolesi Jirga, the lower house of parliament, for a vote.
Twelve of the 25 positions in Karzai's cabinet are unfilled, so these latest nominations would fill roughly half of the vacant positions.
Karzai has struggled to get his nominees approved by parliament since beginning his second term in November.
The Wolesi Jirga rejected 17 of his first 24 nominees in early January, then vetoed another 10 nominees two weeks later.
Karzai also needs to appoint a new head of the National Directorate of Security (NDS), Afghanistan's spy agency. Amrullah Saleh, the former NDS chief, resigned along with Atmar earlier this month.