The defending champion's time of 26.62 seconds broke his previous mark of 26.67 seconds, set at the world championships in Rome in 2009.
Britain's Adam Peaty, who beat Van der Burgh to the 100m breaststroke gold on Monday, was the second fastest qualifier for Tuesday night's semi-finals in a time of 26.68.
According to news reports the rivals are set to resume their battle over the shorter distance in tonights semi and Wednesday’s final.
This is the fifth time a world record has been broken in Kazan and it is the first time a men’s record has been broken at a world championship since 2011.
Sweden’s Sarah Sjostrom broke the women’s 100m butterfly record twice in the space of 24 hours en route to retaining her world title on Monday.
Hungary’s Katinka Hosszu broke the women’s 200m individual medley record as she won gold on Monday night and Katie Ledecky of the USA bettered her own 1500m freestyle record in Monday morning’s heats.
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