The home-based Super Eagles have failed to qualify for the 2020 Championship of African Nations in Cameroon.
The Eagles had lost 4-1 in the first leg match played a fortnight ago in Lome and needed an outright 3-0 win to secure qualification but failed to achieve that.
The second leg ended 2-0 in favour of the Super Eagles B courtesy of a Sikiru Alimi brace but Nigeria lost 3-4 on aggregate to crash out, leaving head coach Imama Amapakabo with plenty of questions to answer.
The game, played at the Agege Stadium in Lagos, saw the Nigerian side dominating the proceedings and it paid off early in the game as the Lobi star forward Sikiru Alimi opened scoring inside 10 minutes.
All the efforts of the Eagles B team to add to their tally in the first half proved abortive as the Togolese stood their ground throughout the first half.
The second half resumed with the Nigerian side still probing the visitors and eventually had the ball at the back of the net through Ndah but the referee ruled it as offside.
Alimi completed his brace in the 71st minute of the game and increased the hopes of the millions of Nigerians rooting for the team.
However, the Nigerian side failed to make the added 10 minutes count as they failed to add to their tally.
It means Nigeria, who finished as runner up in the last edition in Morocco will not be playing in Cameroon in 2020 as Togo progressed 4-3 on aggregates.
The Agege Stadium has witnessed two teams fail to progress to tournaments after the Super Falcons also saw their Olympics hopes crushed by Cote d’Ivoire last month.