It was the South African's first major competition after a long road back to recovery blighted by a string of injuries.
But he crashed out of the men’s 400m in the semi-finals, a disappointing turn for the 29-year-old, who had set a world record on his way to gold at Rio 2016.
Van Niekerk partly attributes the failure in Tokyo to a lack of concentration: “I had an issue with my back, and I know now my mind was not centred, and that can set you back,” he told South Africa’s News24.
“I didn’t get to execute my race as well as I’d have liked to because there was a mental aspect that I hadn’t considered.”
The two-time world champion remains hopeful that he will recover his form and focus for the 2022 World Athletics Championships in Oregon as well as the 2022 Commonwealth Games in Birmingham.
Van Niekerk: It's been crazy and tough
Before lining up at the Olympic Stadium in Tokyo, the 29-year-old who had to postpone his planned comeback in 2019 for the World Athletics Championships due to bone bruising on his knee.
In October 2017 the South African runner ruptured the anterior cruciate ligament in his right knee while playing in a charity touch rugby match in Cape Town.
He has since struggled for consistency.
“Looking back at this year, in so many ways it’s really been crazy and generally tough. Not only did the COVID-19 pandemic create inconsistencies with socialising and interaction, it also affected our fitness,” he said.
Van Niekerk, who was relieved to have qualified for Tokyo, finished fifth in his semi-finals won by Bahamas' Steven Gardiner, who went on to win gold in the final.
Looking ahead to 2022
Team South Africa ended the Tokyo Games without a single medal from the track and their star sprinter knows exactly what he needs to fix to put his country back on the limelight.
“To get to where I want to be, I have to compete more. It’s practice. I know it’s not really an endurance issue, it’s a consistency issue.”
Van Niekerk, who told Olympics.com that the knee injury had strengthened his mental toughness, remains optimistic of bouncing back next season.
“I believe the upcoming season and year will definitely be the perfect opportunity for me to polish up on what I messed this year. I don’t think I am that far off from where I need to be and it is not much of a worry for me,” Van Niekerk who is now based in Florida told the South Africa's Sowetanlive.
He added: “If I look at the races I ran this year in South Africa, in the 200m I clocked between 20.01 and 20.03.”
“When you also look at my race in Spain, I came close second to the silver medalist this year at the Olympics.
“I am an athlete who goes hard from the get-go and in the semi-finals that is what I was trying to do but unfortunately it didn’t work the way I wanted.”