He saved Bertrand Traore's effort from the spot in the deciding penalty shootout to secure victory.
However, the Pharoahs advanced 4-3 on penalties to set up a mouthwatering final clash between Egypt and the victor between Ghana and Cameroon, this was after exhausting the extra time.
"Burkina Faso are strong and they placed us under pressure".
AS Roma's Mohamed Salah scored the first goal in the 65th minute of the match.
After that goal by Aristide Bance, Burkina Faso became the first team to breach Egypt's defence in the 2017 AFCON.
"We knew it would be hard because Burkina were powerful and very quick", he said. After Egypt broke out of defense quickly, the ball fell to Salah on the edge of the penalty area and he sent a sweet left-foot shot curling into the top left corner. Captain Charles Kabore crossed for big striker Bance, who chested the ball down and volleyed it past el-Hadary.
Egypt is the most successful nation in the cup's history with seven titles, followed by Ghana and Cameroon that have 4 titles each. If the Egyptians are winning this final, they will extend their record as the most title winning team with eight cups.
In Gabon el-Hadary arrived as one of Egypt's backup goalkeepers to first-choice Ahmed el-Shenawy.
Egypt's first real opportunity came a little bit late as Trezeguet fired from a long range after 18 minutes, but his curler went inches wide of the target.
With the two teams tied at 1-1, the game stretched into extra time where El-Hadary proved his experience keeping out shots from Prejudice Nakoulma and Bonau Diawara with the seven-time African champions prevailed 4-3. Both Ghana and Cameroon have won four African Cups, the teams with the next-best records behind Egypt.