Ursula von der Leyen made the announcement as Chancellor Angela Merkel prepared to meet President Francois Hollande in Paris.
The leaders will discuss support in the wake of the deadly attacks by Islamic State in the French capital.
Around 1,500 French troops are deployed in Mali to fight against militants.
"We will and must stand firmly by France's side," Ms von der Leyen said.
The deployment comes after France invoked a previously unused EU treaty clause in the wake of the Paris attacks, which killed 130 people.
The clause obliges other member states to provide it with "aid and assistance by all means in their power".
Germany's move also follows an attack last week by al-Qaeda linked militants on a hotel in Mali's capital Bamako, killing 22 people.
French forces have been present in Mali after they intervened to push back an advance by al-Qaeda linked groups that seized control of the country's north in 2012.
However, large parts of the country remain beyond the control of government and foreign forces.
Ms von der Leyen said the German soldiers would focus on logistics and reconnaissance as part of the UN peacekeeping mission in Mali (Minusma).
France would "no longer be so tightly bound to this part of the world" if the international mission can boost stability, she added.
Germany currently has nine soldiers in Minusma and 200 involved in an EU training mission in the quieter south of the country.
The country has also increased the number of its troops training Kurdish Peshmerga forces in Iraq.
Germany will send up to 650 soldiers to Mali to support France in its fight against Islamist militants, the country's defence minister has said.