In a statement issued by his office, Karzai regretted the latest rejection.
"In introducing the nominees to parliament a second time, Karzai considered the ministers to be competent and professional and when they did not receive a positive result, he regrets that," the statement said.
Karzai submitted a first list of minister candidates to parliament earlier this month.
Parliament then rejected 17 of 24 nominees and the president was forced to present a new list of names for the posts yet to be filled.
During more than a week of hearings, legislators have complained that the new nominees were even less qualified than the previous ones, and said that most were selected because of their ties with major political power brokers.
Shukria Barakzai, a member of parliament, said a line seemed to have been drawn between those legislators who were not impressed with Karzai's cabinet line-up and those who wanted to finalise the government.
Karzai is under pressure to have a government in place ahead of an international conference to be held in London on January 28 to discuss the country's future.
Karzai was re-elected in an August presidential poll marred by allegations of fraud.