Senegal’s win ended the Eagles eight-game unbeaten run since their exit from the 2018 World Cup in Russia.
Idrissa Gueye grabbed the match winner for the Teranga Lions in the 20th minute of the game, which was played behind closed doors.
The Everton midfielder capitalised on a defensive mix up to hand his side the lead. Nigeria came close to drawing level on a number of occasions through Odion Ighalo and Wilfred Ndidi before the interval.
At the start of the second half, Samuel Chukwueze was denied a goal in his third start, when his close-range shot was blocked with a last-ditch tackle, while substitute Oghenekaro Etebo’s free kick on the edge of the box rattled the crossbar.
Gernot Rohr made six changes to his team as they searched for an equaliser. The German introduced Ola Aina, Henry Onyekuru, Moses Simon, Victor Osimhen and Chidozie Awaziem for Jamilu Collins, John Ogu, Chukwueze, Alex Iwobi, Ighalo and Samuel Kalu, but they failed to earn a share of the spoils.
The win was the first for Senegal against Nigeria in 17 years. The last time was at the AFCON in 2002, when Papa Bouba Diop and Salif Diao secured a 2-1 win over Nigeria in the semi-final. Julius Aghahowa scored a consolatory goal in the 89th minute in that game.
The Eagles, who will be making their 18th AFCON appearance in Egypt, will depart from Ismailia on Monday morning for Alexandria – venue of their Group B games against Burundi, Guinea and Madagascar.