Yattara swept in the opener from a corner before Christophe Nduwarugira was sent off for Burundi after committing a foul as the last man.
Yattara made the win safe in the second half with a composed strike.
Guinea must now wait to discover if they will progress as one of the best third-placed teams.
They finish the group stage with four points. The four third-placed sides with the best records will go through.
Madagascar’s 2-0 win against Nigeria meant the Africa Cup of Nations debutants topped Group B with the Super Eagles progressing to the knockout stage as runners-up