Khune, a star performer for club and country, has been put forward for two prizes - the South African Sportsman of the Year and the Sport Star of the Year respectively.
The reigning PSL Footballer of the Season faces competition from Proteas batsman Hashim Amla and Olympic gold medallist Cameron van der Burgh in the first category, with Amla, Chad le Clos, Lucas Sithole and Mapaseka Makhanya in contention for the other accolade.
Amakhosi, by virtue of their Premiership and Nedbank Cup triumph last season, are also in the running for the Team of the Year award along with the Proteas and the Springboks, while Fran Hilton-Smith, the acting technical director of Safa, has been nominated for the Sports Administrator of the Year prize. She is up against South African Rugby Union chief executive Jurie Roux and Netball South Africa president Mimi Mthethwa.
"Just being a nominee is a big win in itself, it just shows I am doing something right and gives me the motivation to work even harder," Khune is quoted as saying by Safa's official website.
"I am very delighted to have made it among the top and I would like to thank the minister of sport (Fikile Mbalula) and all those working with him for this noble iniative.
"There is no better honour than being appreciated in your own country. I also want to wish the best to everyone who has been nominated, and as for those in my categories I believe whoever wins will be very deserving as they are also strong in their own sporting disciplines."
Hilton-Smith, a former Banyana Banyana coach, added: "I am truly humbled and have welcomed the nomination after years of hard work in administration. My contribution towards the development of women’s football over the years has enabled women’s football to grow and be where it is today.
"Now in my role as the technical director, I want to see the same growth in the men’s teams, with the junior teams qualifying for the World Cup."
The awards ceremony will take place at Sun City next month.