Eswatini trail 1-2 at half time of the match against Guinea-Bissau in the 2021 AFCON Qualifier at the Mavuso Sports Centre.
Marcelo Djalo out the visitors ahead in the 15th minute before Felix Badenhorst leveled matters four minutes later for the hosts.
However, Guinea-Bissau had other ideas as Alfa Semedo made it 2-1 in the 24th minute.
In the second half, Pele added the third goal in the 50th minute for the coach Baciro Cande-led side.
Eswatini have one point and wind up the group’s qualifiers by facing already qualified Senegal next week.
Senegal booked their place at the finals with 12 points from four games, Congo are second with seven points, three for Guinea-Bissau and one point for Eswatini.