The former Proteas allrounder will take over the reins from Stephen Fleming, who stepped down from the role earlier this month and will take over as England's Test mentor.
Morkel had worked under Fleming and previously spent many years as a player with the Chennai Super Kings in the Indian Premier League (IPL).
"It is an incredible honour to be appointed Head Coach of the Joburg Super Kings," Morkel said in a statement. "From wearing the Super Kings jersey as a player to now leading one of its franchises as Head Coach, this journey is truly special.
"I look forward to building on the strong foundations we've created together and helping this group achieve its full potential."
The Super Kings have not yet won the SA20 trophy, reaching the semifinals in 2023 and 2024, while they were knocked out in the Eliminator in 2025 and 2026.
Kasi Viswanathan, JSK director, added: "Albie Morkel understands our culture well, having experienced it both as a player and as a coach.
"His leadership and understanding of the South African cricket landscape gives us great confidence as we move forward."
The fifth season of SA20 kicks off 17 January 2027 with Joburg Super Kings starting their campaign against Paarl Royals the following day.
Joe Root is set to return for season 5 of SA20 with Paarl Royals while Australia T20I captain Mitchell Marsh will make his debut in the tournament with Sunrisers Eastern Cape.
Sunrisers Eastern Cape and Pretoria Capitals will open the fifth Betway SA20 season on Sunday, 17 January 2027 at St George's Park in Gqeberha.
Sunrisers Eastern Cape underlined their status as SA20's dominant force with a nerve-shredding six-wicket victory over Pretoria Capitals at Newlands, clinching a third title in four seasons.
Sunrisers Eastern Cape sailed into yet another SA20 final after beating the Paarl Royals by seven wickets in a low-scoring encounter at the Wanderers on Friday.
