Merkel later heads to Niger and then Ethiopia where she is to visit the African Union headquarters in the capital Addis Ababa.
Her talks with leaders of all three countries are to focus on migration issues and the battle against terrorism.
“I believe we must take a far greater interest in Africa's destiny,” Merkel said in her weekly video podcast Saturday. “The well-being of Africa is in Germany's interest.”
She earlier told Die Zeit weekly that bringing more stability to Africa and improving living conditions on the continent would help reduce the numbers of people seeking to leave.
In Mali, Merkel was also due to visit German troops taking part in the UN peacekeeping operation MINUSMA and the European Union Training Mission in Mali. Next week, back in Berlin, Merkel will host Chadian President Idriss Deby and Nigeria's President Muhammadu Buhari.
The German leader has said that she wants the European Union and North African countries to do deals modelled on a controversial agreement with Turkey to curb migrant flows to Europe.
Under the EU-Turkey deal, Ankara agreed to take back Syrians who made it to Greece in return for being allowed to send refugees from its massive camps to the bloc in a more orderly redistribution programme.
The pact also pledges billions of euros in EU aid for Turkey and visa-free European travel for Turkish citizens.