"African startups have energy but the big providers of development aid and financiers have not adapted to that. We ourselves are too slow, too hesitant," Macron said when announcing the scheme.
The third VivaTech features speeches by Facebook CEO Mark Zuckerberg and Uber boss Dara Khosrowshah, who met Macron on Wednesday, and has focused on Africa's startup scene.
Rwandan President Paul Kagame attended the event.
African startups raised some 477 million euros in 2017, up more than 50 percent in a year, according to an estimate by investment fund Partech Ventures.
The figure is still dwarfed by the estimated 20 billion euros raised by European startups in the same period.
The French development agency AFD will set up a fund "to fill the gaps in the support with small sums ranging from 30,000 to 50,000 euros, which is what startups need", Macron said.
The AFD also aims to bring other donors on board "to grow this initiative tenfold," Macron said.
Entrepreneurs will be able to apply for funding through the AFD's Digital Africa platform.