Guinea-Bissau took control of Group L in the 2027 Africa Cup of Nations qualifying series, thanks to a 3-0 drubbing of Nigeria in Bissau.
Both teams came into the match having won their opening fixture and looking to take early leadership.
The Super Eagles failed to threaten the hosts for most of the first half before the Djurtus eventually took the lead.
Franculino Djú escaped down the right hand side and dribbled past Bruno Onyemaechi before shooting past Stanley Nwabali.
Guinea-Bissau doubled their lead in the 66th minute of the match through Mama Baldé, before adding a third in stoppage time.
They are now three points clear at the top of the group, with Nigeria in second place with three points.