In another game, Tunisia claimed a 5-2 win over Libya to ensure they seal top position in the group
Emilio Nsue scored the only goal of the game as Equatorial Guinea defeated Tanzania 1-0 to advance to the Africa Cup of Nations, and send the Taifa Stars crashing out of contention.
In a match staged at the Nuevo Stadium in Malabo on Thursday, the National Thunder needed maximum points to qualify from Group J, while the East Africans needed a win to revive their chances of making it to the finals.
Taifa Stars, under then head coach Etienne Ndayiragije, had managed to win the first match between the pair 2-1, when goals from Simon Msuva and Salum Abubakar were enough to give them a win over their opponents, who had scored through Pedro Obiang.
Coming into the Thursday night game, the East Africans knew they had to give their best and get a positive outcome to stand a chance of making it to the finals alongside Tunisia who had qualified with two games to spare.
Kim Poulsen's charges resorted to cautious play especially in the first half, and struggled to get into the opponent's danger zone, appearing content instead to secure a point away to take qualification to the final day.
It seemed they had done enough until concentration lapses in the 90th minute allowed Nsue to grab the winner.
In the Group J game, Libya suffered a 5-2 loss at home against Tunisia.
It was the hosts who started the game on a high and needed 21 minutes to get their opening goal courtesy of Muaid Ellafi. However, the Carthage Lions replied in the 39th minute through Ellyes Skhiri.
The visitors scored their second in the 48th minute thanks to substitute Seifeddine Jaziri's strike. Mohamed Drager made it 3-1 three minutes later before Ellafi completed his brace in the 54th minute in favour of the hosts.
Another substitute, Anis Ben Slimane ensured Tunisia sealed the win as he found the back of the net with six minutes to go. By the time Jaziri scored the fifth, the Libyans were already out of the game.
Tanzania will now play Libya at home as a formality since Tunisia and Equatorial Guinea have already qualified.
Equatorial Guinea XI: Jesus Owono, Marvin Anieboh, Federico Bikoro, Igor Engonga, Jose Machin, Luis Alberto Meseguer, Josete Miranda, Basilio Ndong, Salomon Obama, Pedro Obiang, Esteban Orozco.
Subs : Aitor Embela, Marcos Ondo, Ebang Ela, Vicente Esono, Angel Miguel, Emilio Nsue, Jannick Buyla, Saul Coco, Pablo Ganet, Jordan Nsang, Joanet Lopez, Ruben Belima.
Tanzania XI: Aishi Manula, Hussein Mohammed, Shomari Kapombe, Kennedy Juma, Jonas Mkude, Simon Msuva, Erasto Nyoni, Faisal Salum, Mbwana Samatta, Iddi Selemani, Yassin Mzamiru.
Subs: Juma Kaseja, Bakari Mwamnyeto, Kelvin Yondani, Israel Mwenda, Salum Abubakar, Hassan Dilunga, Ayoub Lyanga, Himid Mao, Farid Mussa, Thomas Ulimwengu, Nickson Kibabage