The Falcons had earlier defeated their Mali by a lone goalscored by Under 20 Striker Rasheedat Ajibade.
A semi final place was already secured after the Falcons beat Senegal in their second group match.
Newly Unveiled Super Falcons CoachThomas Dennerby, who was in charge for the encounter, decided to rest top scorer Ajibade for the match against Togo, who lost 6 - 0 to Senegal in their opening match.
The Falcons continued from where they stopped as Anam Imo scored in the 40th minute to give Nigeria a first half lead.
The Falcons then doubled their lead through Uchendu Chinaza in the 48th minute, Chioma Wogu scored Nigeria's third in the 71st minute, but the Togolese pulled one back through Woedikou Afi.
The result sees the Super Falcons top the group with nine points fro three games, while Mali defeated Senegal 1- 0 in the other group game to finish runners up to Nigeria.
WAFU Women's Cup Semi-final fixtures
The WAFU Women's Cup semi final will take place on Thursday, February 22
Ivory Coast vs Mali (4pm Nigerian time)
Nigeria vs Ghana (7pm Nigerian time)