As some 80 leaders from the two continents kicked off a mammoth summit that locked down parts of Brussels, France and Germany announced a new partnership for Africa aimed at promoting peace and development as well as combatting the effects of climate change.
Chancellor Angela Merkel said Berlin and Paris were "seeking to be a motor" in Africa's development as well as its security.
Germany, long reticent to take part in military missions, was on "a new path", Merkel said.
"We want to deploy our friendship on the ground," said French President Francois Hollande, adding that it was thanks to Germany that the European Union finally had been able to announce the launch of a delayed military mission to send 800 troops to the Central Africa Republic (CAR).
Delayed due to insufficient troop and aircraft commitments from member states, the launch of the EU operation in CAR was announced on the eve of the EU-Africa summit, which winds up on Thursday.
Germany has contributed air transport, with Georgia, Spain, France, Estonia, Finland, Italy, Latvia, Poland and Portugal providing troops and Britain, Luxembourg and Sweden logistical support.
As chaos worsens in CAR, a score of leaders from the 54-member African Union and 28-nation EU gathered with United Nations Secretary General Ban Ki-moon to discuss the crisis.
"We are deeply concerned of the desperate plight of the people of the CAR," said Ban, who is seeking Security Council endorsement for a 12,000-strong peacekeeping force to take over from the 8,000 African and French troops there.
UN Head Ban Ki-Moon has warned the situation could spiral into genocide amid reports by the UN of child decapitations, cannibalism and widespread lynchings. Around a million people, a quarter of the population, have been displaced.
Trade has been another cause of tension as the two blocs struggle to agree deals that would give Africa better access to EU markets while lifting African tariffs seen as a vital source of state income and a needed protection to its fledgling industry.
The EU continues to be Africa's largest donor but now is looking to switch from its historic role of providing assistance to a more dynamic one of investor.
"The need for investment in Africa is so huge that the more investment coming, the better," said EU Development Commissioner Andris Piebalgs.