The runner won gold in the 400m, finishing with a time of 43.03.
Van Niekerk had handwritten on his shoes the words 'Jesus I’m all yours use me'.
Speaking to the BBC after his victory, he said: 'The only thing I can do right now is give God praise.
'I went on my knees each and every day and asked the Lord to take care of me. I even wrote it on my spikes (shoes).
'I asked the Lord to carry me through the race and I’m really pleased and grateful for this opportunity.'
In March the runner became the first person to have dipped below 10 seconds in the 100m, 20 seconds in the 200m and 44 seconds in the 400m.
Van Niekerk repeatedly thanked God in the post-race press conference.
Afterwards, he posted on Instagram:
Speaking last year, the athlete told Passion for Sport, 'It's all thanks to the Lord. Everything that comes my way, I thank the Lord. I live every race and step of the way in his hands. I trust him in everything I do.'
He added that God was 'the one who blessed me with this talent and put me in my mother's womb.'
He also talked about the importance of 'growing spiritually each day' and recognising 'the powerful God out there pushing us all to the next level'.