Mbokazi has signed a four-year contract with MLS side Chicago Fire and will officially join the club in January.
His departure comes less than a year after being promoted from the DStv Diski Challenge side and months after being named co-captain alongside Nkosinathi Sibisi. The 20-year-old bows out having lifted the Carling Knockout Cup as skipper last weekend.
Ndah praised Mbokazi's ability, personality and impact, emphasising how the youngster transformed Pirates' defensive structure.
"It's a very big loss for us, but for him personally it's growth in his career," said the Nigerian while speaking on Metro FM Sports Night Live.
"We all love him. From the first time I watched him in the DDC, he stood out. He's very funny - you don't know how funny he is. He's troublesome, always looking for trouble, looking for me or Makhehleni Makhaula or someone. That's just the vibe he brings."
Ndah was full of admiration for how quickly the young defender established himself as an indispensable figure.
"The whole team loves him, and it's going to be a big miss because since he stepped in, he's been doing wonderfully well," he noted.
The dreadlocked defender also reiterated his belief that Mbokazi is currently the best centre-back in the country, and despite his departure, Pirates still have the depth to cope.
"I said this the last time - for me, he's the best centre-back in South Africa right now. You can see why. We've conceded around five goals. It's not just him; it's the whole team, but he's been a big part of that," he added.
"Even when Sibisi or Thabiso Sesane - who's back now - steps in, there are a lot of players I'm confident can fill the void."