Ana Paula Tuavanje Elias had been appointed in October 2019 and will be replaced by Luísa Maria Alves Grilo.
Jesus Faria Maiato had been appointed in October 2017, replacing António Rodrigues Afonso Paulo, who did not attend the inauguration ceremony.
For his place, João Lourenço has now chosen Teresa Rodrigues Dias.
The President also dismissed Manuel de Jesus Moreira from the post of Secretary of State for Labor and Social Security, a role that will be assumed by Pedro José Filipe.
The justification for substitutions is only "convenience of service".
In another presidential decree, João Lourenço appointed Maria Cândida Teixeira as ambassador to Cuba.