The 46-year-old Duarte was in charge of Burkina Faso from 2008 to 2012 but fired for "unsatisfactory results". He has also coached Gabon and last worked at Tunisian club CS Sfaxien.
Rohr quit earlier this month as coach to take up television work and a role with the football association in his native Germany. Burkina Faso last month booked a place in the group phase of Africa’s qualifiers for the 2018 World Cup by beating Benin 3-2 on aggregate over two legs.
They next play in March in the 2017 African Nations Cup qualifiers with back-to-back home and away group games against Uganda.
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(Reporting by Mark Gleeson in Durban; Editing by Amlan Chakraborty)
