After falling behind five minutes from time, the White Knights levelled six minutes into additional time through Osama Faisal and Ahmed Sayed converted a 116th-minute penalty to win the tie.
Zamalek meet fierce rivals Al Ahly Friday in the first final of the CAF Champions League involving two clubs from same country since the competition was launched 56 years ago.
Here, we round up all the football news from Africa:
Al Ahly also booked an Egyptian FA Cup semi-final spot, but in a different manner to Zamalek as they overcame second-tier Abu Qir Fertilizer 2-1.
Veteran Walid Soliman bagged a brace for record eight-time African champions Ahly, with the second goal coming from a penalty, before conceding late in the opening half.
Ahly will meet Al Ittihad and Zamalek face Tala'ea el Gaish in the semi-finals on December 1 with the final four days later.
Defending champions Simba crushed Coastal Union 7-0 to move within two points of leaders Azam and Young Africans after 11 rounds of the Tanzanian Premier League.
Tanzania international John Bocco scored a 14-minute hat-trick as Simba built a five-goal lead by half-time and Zambian Clatous Chama bagged a second-half brace.
Azam fell 1-0 at Kinondoni Municipal Council while record 22-time champions Young Africans were held 1-1 at home by Namungo.
A Themba Zwane hat-trick helped Mamelodi Sundowns edge AmaZulu 4-3 and retain first place after four rounds of the South African Premiership.
Sundowns have 10 points as they chase a record fourth consecutive title, two points more than Soweto clubs Swallows and Orlando Pirates.
Bottom side Maritzburg United reacted to a 1-0 loss at Black Leopards -- their fourth in a row -- by firing coach and former South Africa coach Eric Tinkler.
French coach Francois Ciccolini has been fired following his competitive debut with USM Alger for refusing to participate in a medal ceremony after a 2-1 loss to CR Belouizdad in the Algerian Super Cup match.
USM chairman Achour Djelloul was furious at the snub to Prime Minister Abdelaziz Djerad, saying: "Ciccolini made a mistake and has to pay. We have decided to fire him."
Ciccolini, 58, had been set for a second spell with an Algerian club having been in charge of JS Kabylie for two years from 2014.
Former Ivory Coast icons Didier Drogba and Yaya Toure have hailed national football federation president Augustin Sidy Diarra, 61, who died at the weekend after contracting Covid-19.
"The Ivorian, African and world football family has just lost one of its sons," tweeted Drogba, a contender in delayed elections for the federation presidency.
Toure said on Facebook: "We are devastated by this sad news which shocks the entire football world in Cote d'Ivoire."
Green Eagles are the Zambian Premier League pacesetters with a 1-0 home win against bottom club Kitwe United giving them a two-point lead over Forest Rangers and Buildcon after five rounds.
Anos Temba scored 16 minutes from time for Eagles, who finished third last season to qualify for the CAF Confederation Cup, the African equivalent of the UEFA Europa League.
Defending champions Nkana are languishing in 11th place after a 1-1 home draw with Zanaco, who retained an early lead for 54 minutes before Freddy Tshimenga levelled.
Togo is mourning the losses of former Confederation of African Football (CAF) vice-president General Seyi Memene and Toyi Awi, a winger with champions ASKO Kara.
Former government minister Memene retired from CAF in 2011 "after years of dedication and commitment to African football", the Cairo-based organisation said.
Awi, who was preparing for a 2021 CAF Champions League match against Racing Club Abidjan of the Ivory Coast this weekend, collapsed clutching his chest, and died en route to hospital.
Standout matches today