With the score tied at 1-1 after 120 minutes of football, Algeria defeated Ivory 4-3 via penalty shoot-out to advance to the semi-finals.
They will battle the Super Eagles at the Cairo International Stadium on Sunday for a place in the final of the continental showpiece.
On Wednesday, Gernot Rohr's men advanced into the last four after edging South Africa 2-1 in Cairo.
The two countries have met six times on the international scene with Nigeria unbeaten in a run of five wins and a draw.
Algeria last won the tournament in 1990 - their first and only triumph on the continental stage while Nigeria have won the title three times in 1980, 1994 and 2013.