The Bafana Bafana right-back was also chosen as the Players' Player of the Year.
“I’ve been with City for three seasons and have enjoyed being part of a talented squad who love to play free-flowing football and who have a never-say die attitude,” said Mkhize.
“We’ve finished third, fifth and fourth in the league and will be aiming to go all the way next season.
"I just want to thank the club and the supporters for their unwavering support.
"Coach Benni (McCarthy) is a real inspiration to us all and wants us to be the best we can, and that’s always a work in progress. To be honoured with two awards could not have been possible without my teammates, who have given it their all in pursuit of our goals.”
Winger Gift Links won the most improved player of the season, while defender Zukhile Kewuti was named rookie of the season.
Durban-born Mkhize played 34 matches in all competitions for City this season and scored three goals - one in the league and two in the Nedbank Cup.
The 30-year-old led his side to victory in the MTN8 knockout tournament earlier in the season and to a fourth place finish in the Premiership.
Mkhize has been a regular starter for City since the day he arrived at the club from Maritzburg United in 2016.
Under then coach Eric Tinkler he played from game one and has become a force to be reckoned with.
How Orlando Pirates must be ruing not letting him go after agreeing and then terminating a three-year contract with the then Maritzburg defender.
This season Mkhize has led from the front and it was no surprise when he was recalled to the national squad. He is set to be part of coach Stuart Baxter’s Bafana squad for the Africa Cup of Nations tournament starting in Egypt on June 21.
Teko Modise was also honoured at the awards evening held at the Radisson Blu Hotel in the V & A Waterfront.
The 37-year-old, who made 66 appearances for Bafana Bafana (10 goals, first on debut in 2007), announced his retirement at a hastily arranged media conference.
“The body aches and after much thought I’ve decided to call time on a career that has given me all I could have wished without any regrets. If I could do it all over, I wouldn’t change a thing," Modise said.
“I played for the biggest clubs like Mamelodi Sundowns, Orlando Pirates and SuperSport United and now with City, and won all the trophies in the PSL, the last being the MTN8 title earlier this season that completed the haul, so what a way to go out.
"But I won’t be gone from the game; I’m in talks with City owner John Comitis to possibly stay on in a role still to be decided.”