The midfielder's crucial 95th minute penalty secured a 2-1 win over Congo in Alexandria, sparking jubilant scenes.
"Also thank you to coach Cuper who has made our dreams come true, " the President was reported to have said.
Liverpool star Mohamed Salah was the hero with a brace as the Pharaohs reached the finals for the first time in 27 years, in the process ending Ghana's feint hopes of qualification.
"I'm proud of all the players but especially of Mo Salah who was fearless enough to take the crucial penalty", the president said.
But former Chelsea player Salah, 25, stepped up to convert the spot kick and send the Pharaohs to Russian Federation 2018.
He said after the game, "I can't really express how I feel, I don't quite talk so much but I'm really proud", "Today we realized a long-awaited dream".
Despite the support given to the national team by Egyptians and Arab fans who celebrated the win, football clubs in Egypt have not enjoyed such support since their vital role during the uprising of 25 January 2011.
"The match was hard, thank god that we made it". It all happened because of everyone's support, " the former Al Ahly winger concluded.
Speaking earlier this year, Sisi blamed the country's woes on Egypt's overpopulation crisis as one of the major challenges confronting the state, saying that the population is now four and a half times what it was in 1952.