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Cape Town-born Van Niekerk, who shattered the 400m record at the Rio Olympics in August, beat fellow track superstar Caster Semenya and cricketer Kagiso Rabada to the honours.
It was the second successive year that Van Niekerk, 24, got the top award at this event. He was also named sportsman of the year and also received the Shield of Jove, confered on best SA athlete of the Olympics.
He also got the international recognition award alongside Semenya, Rabada, Seabelo Senatla (Sevens Rugby) and Brad Binder (motorsport).
Van Niekerk has had a highly successful year, having clocked 43.03 in the 400m in Rio to set a new record, displacing that of Michael Johnson (43.18), which had stood since 1999.
Only a fortnight ago he was honoured by the Association of National Olympic Committee as the best male athlete of the Rio Games.
Semenya may have lost out on the biggest award of the evening but, fittingly, she walked away with the sportswoman of the year gong.
Like Van Niekerk, she had a great year, winning Olympic gold in the 800m and also became the first athlete to win the 1 500m, 800m and 400m at the SA Champs in April. Van Niekerk's coach Ans Botha was named coach of the year, beating Mamelodi Sundowns coach Pitso Mosimane, Jean Venter (athletics) and Suzanne Ferreira (para-athletics). Sundowns were named team of the year after clinching the CAF Champions League and the Absa Premiership this year.
Other winners include teenager Ntando Mahlangu, who won silver in the 200m T42 race at the Paralympics; Charl du Toit won sportsman of the year with a disability; Ilse Hayes won that award from the women's side. Benny Sports Academy were honoured for developing local footballers.