The world 400m world record-holder knocked 0.03 seconds off Anaso Jobodwana’s previous South African record to go top of the global leader board.
“This is definitely a positive step forward, I felt that I was in pretty good shape last week in Boston, I wanted to repeat that here,” Van Niekerk was quoted by the IAAF website.
Van Niekerk posted the exact same time he clocked last weekend on a 200m straight-track at the Boston Games which could not be considered for record purposes.
The Racers Grand Prix in Kingston is part of Usain Bolt’s farewell tour where he raced in his final 100m on home soil.
Bolt won his race in a time 10.03 with countrymen Jevaughn Minzie and Nickel Ashmeade finishing behind him in 10.15 and 10.18 respectively.
Van Niekerk finished ahead of Jamaicans Rasheed Dwyer (20.11) and London 2012 bronze medallist Warren Weir in 20.18.
Two years ago Van Niekerk became the first South African to break through the 20-second barrier in the 200m when he blitzed to a time of 19.97 in a ‘B’ final at a meeting in Lucerne.
Jobodwana then lowered the record to 19.87 for his bronze medal at the IAAF World Championships in Beijing.
Van Niekerk's form in the half-lap event bodes well for his bid at the World Championships in London where he will attempt the 200-400m double.
The IAAF has approved changes to the timetable for the August Championships following requests from South Africa to enable Van Niekerk to attempt the double.
Van Niekerk, who shattered Michael Johnson’s 400m world record at the Rio Olympic Games when he crossed the line in 43.03 seconds, has been conservatively racing his specialist one-lap event.
He will be racing in his first international 400m race of the season at the Diamond League meeting in Lausanne in July.
The South African will be looking to make a strong statement in his specialist event and knock a big chunk off his season’s best time of 46.28.
Earlier, South African 100m record-holder Akani Simbine finished second (10:00) behind former Jamaican world champion Yohan Blake (9:97) in the short sprint.
Meanwhile, continuing on her good form South African-based Briton Tish Jones captured the Durban leg of the Spar Women’s 10km Challenge with a new personal best time.
The Cape Town Marathon champion led from gun to tape andcross the line first at the King’s Park Stadium in 32.58 minutes. She finished ahead of Kesa Moletsane, who launched a late charge to finish in second place (33.31). Lebogang Phalula took third in 33.39.
Jones also won the Cape Town One Run last month.
“As soon as the start gun went off I found myself in the lead and I wasn’t sure how sensible that was but I know I am comfortable going out at that pace now,” Jones said.
“I guess I was just contemplating what would happen to everyone after five kilometres and whether I can maintain that pace.”
Jones had Zimbabwe’s Rutendo Nyahora, Nolene Conrad and Ethiopian Elisabet Arsedo for company in the first half of the race. She made her
break close to the six-kilometre mark as she opened a decent gap which she held to the finish.
Back in April, Jones earned 18th place at the London Marathon with a personal best time of 2:33:56. It was only her second 42km race.
“Running a marathon at a fast pace for 42 kilometres lends itself to doing a 10km but a 10km is nerve-wracking for me,” Jones said.
Moletsane, who won the Port Elizabeth race of the six-leg series, said she had to adapt to the change in temperatures coming from the freezing Free State to the warmer Durban.
“Things did not go well, I didn’t feel like myself but I pushed hard to ensure I finish in the top three to stay in contention in the series,” Moletsane said.