He edged out fellow Christian athlete Kirani James to win in Rio on Sunday night.
Speaking to 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."
Handwritten on his spikes were the words "Jesus I'm all yours use me".
Gold in Rio follows on from victory at the World Championships in Beijing last year.
Earlier this year he became the first man ever to run a sub-10 second 100m, sub-20 200m and sub-44 400m.
While gold was always on the agenda, it was his world record 43.03 seconds that shocked many in Rio.
The previous best over 400m by Michael Johnson had stood for 17 years.
Wayde van Niekirk has previously spoken openly about his Christian faith.
Speaking to Premier's media partner Passion for Sport before the Olympics, he said: "Everything that comes my way I thank the Lord.
"I leave every race, every step that I take in his hands.
"I trust him in everything I do.
"He's the one that blessed me with this talent."