Parliament voted Saturday to remove Interior Minister Bismillah Khan Mohammadi and Defense Minister Abdul Rahim Wardak, after questioning them about cross-border shelling.
Karzai, in a statement, said Wardak and Mohammadi are "true sons of Afghanistan," adding he had requested them to stay on until replacements could be found.
The two ministries are in charge of conducting the war and directing efforts to bring the country under Afghan control after coalition forces end their combat operations by 2014.
The New York Times reported government officials said the impact of the removal of the two ministers would not be known until it's learned when they will be replaced and how much trust Karzai shows in them until then.
The Times said it was not clear why Parliament decided to dismiss the ministers but quoted some observers as saying the two had failed to award jobs and contracts widely enough.
Pakistani Interior Minister Rehman Malik last week accused Afghanistan of harboring insurgents hostile to Pakistan, a charge Afghans resent as they feel they have been the victims of insurgents from Pakistani havens as well as rocket attacks from within Pakistan, the Times said.
Separately, the Wall Street Journal, quoting analysts and observers, reported Karzai would respect the parliamentary action and find replacements within one month.
"If Karzai wants to appease the international community, he has to respect Parliament's decision," a Western diplomat in Kabul told the Journal. "Especially if he wants Parliament to help him with his new fight against corruption."