The 400m world record holder clocked 30.81 to clip 0.04 off the 17-year-old global 300m mark of 30.85 held by American legend Michael Johnson over the unofficial distance.
He also chopped 0.16 off the meeting record held by Jamaican star Usain Bolt.
While it was the fastest recorded performance over three-quarters of a lap, the International Association of Athletics Federations did not recognise performances over 300m and the time would stand as a world ‘best’ rather than a ratified ‘record’.
Though he had not yet turned out in a top-flight 400m race this season, Van Niekerk again showed he was on track for a rare 200m/400m double at the World Championships in London in August, after clocking a 100m personal best of 9.94 and a 200m national record of 19.84 earlier this month.
Isaac Makwala of Botswana grabbed second spot behind the Olympic one-lap champion in 31.44, and South African teenager Clarence Munyai shattered the world junior 300m best in third position.
Munyai crossed the line in 31.61, becoming the first Under-20 athlete to dip under 32 seconds over the rarely run distance, and shattering his own SA junior best of 32.87.
Meanwhile, Rikenette Steenkamp produced the race of her life, despite struggling to stick with the explosive pace out the blocks in the women’s 100m hurdles contest.
Steenkamp charged through the field in the latter stages to take second place in 12.99.
Though she was well behind German winner Pamela Dutkiewicz (12.72), the diminutive athlete from Pretoria became the second SA woman to crack the 13-second barrier, completing the race 0.05 outside Corien Botha’s 19-year-old national record.
Fellow hurdler Antonio Alkana settled for fourth place in the men’s 110m race in 13.37, after hitting the fifth barrier and failing to recover.
Speedster Alyssa Conley finished second in the women’s 200m dash in 23.03 and middle-distance runner Jacob Rozani ended seventh in the men’s 1 000m race in 2:20.25.