The 21-year-old sustained the injury during training on May 11 and subsequently missed Al Ettifaq's final three Saudi Pro League matches of the campaign and missed out on Bafana Bafana's World Cup squad.
The club announced on Thursday that the operation had been successful, although no details have been provided regarding the nature of the injury or the expected recovery timeline.
"First-team soccer player, Mohau Nkota, underwent a successful knee surgery (on Wednesday)," the club said in a statement.
"The club family wishes the player a speedy recovery, complete wellness, and a quick return to the pitch to continue his journey with the team."
The injury comes at an unfortunate time for the former Orlando Pirates star, who had recently regained his place in the starting line-up after battling for consistency during much of the season.
Nkota arrived at Al Ettifaq last year carrying high expectations following a breakthrough campaign with Pirates. However, adapting to life in the Saudi Pro League proved challenging, with the winger contributing two goals and three assists in 21 league appearances.
Part of that struggle stemmed from being deployed in several positions, including wing-back, a role that often limited his attacking influence. Despite those challenges, he showed signs of improvement in the closing stages of the season before his injury setback.
Nkota's return will also come under a new coaching regime after Al Ettifaq decided not to retain Saad Al Shehri. The 46-year-old guided the club to a seventh-place finish and qualification for the Gulf Club Champions League.
Interestingly, Al Shehri recently singled out Bafana Bafana midfielder Teboho Mokoena for praise, highlighting the Mamelodi Sundowns star's ability to scan the game and make intelligent decisions in possession.
"As a player to make the right decision, attacking or defensive, you must have the perfect vision and read your surroundings," Al Shehri told the Saudi Pro League.
"There is a player from South Africa, and he is exceptional at scanning. He is number four. I have been watching him recently."