Van der Watt, 34, who left his house on his bicycle early on Monday morning, was found roughly 2km from where his canary-yellow bike had been discovered on Wednesday morning.
Police spokeswoman Colonel Priscilla Naidu said police had found his body at about 2pm yesterday.
He had a single gunshot wound to the right side of his head and his service pistol was lying next to him.
His body had to be airlifted from the area.
Naidu said foul play was not suspected.
Earlier in the day, scores of police officers, members of the K9 unit, the Eastern Cape search-and-rescue unit and Mountain Club South Africa, along with other organisations, had continued the search.
Van der Watt, who had last been seen at his home on Sunday, left at 6am on Monday on a cycle from which he never returned.
In the days that followed, social media was abuzz with posts about his disappearance.
His distraught brother, Willem, said yesterday: “I cannot talk right now – it’s not a good time for us. It is very distressing.”
Elzabe Boshoff, the creator of Facebook page “The Heart of an Ironman South Africa” – the title of a book of the same name that she co-authored – said she had found out Van der Watt had gone missing through a cyclist WhatsApp group they both belonged to.
She posted regular updates on Van der Watt’s disappearance and rallied the public to join the search for him.
“The news is devastating, although I never knew him personally,” she said yesterday.
“I also initiated a search on Tuesday from Altona Primary School, where 30 people helped us to search for him.”
Boshoff said that in light of the recent spate of attacks on cyclists, there had been fears that he might also have been attacked.
“At the same time, we hoped that he would be okay,” she said.
Amir Chetty – HeraldLIVE