Esteban Obiang’s 70th-minute goal was all Equatorial Guinea need to end reigning champions Algeria’s 35-game unbeaten streak.
Algeria are likely on their way out of the tournament should they lose their final group match against Ivory Coast.
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The 2019 Cup of Nations winners could only draw 0-0 with Sierra Leone in their opening game in Cameroon and lost 1-0 to Equatorial Guinea on Sunday.
Meanwhile an Equatorial Guinea side ranked 114th in the world and 28th in Africa are now well placed to reach the knockout stages for the third time while the Algeria who is ranked 29th in the world is still struggling to record their first win in the tournament.
The two previous occasions came when they were hosting the tournament, in 2012 and in 2015, but this time many of the fans in the crowd of almost 12,000 in Douala were supporting the ‘National Thunder’.