The Dutchman, who caused a major upset by beating the Australian at the 2000 Olympics, led the way through both the morning's heats and the evening's semi-finals, with Thorpe second-fastest overall each time, although the two did not race head to head.
Van den Hoogenband clocked one minute 47.21 seconds in the heats and 1:46.32 in the semi-finals, swimming inside Thorpe's world record split for the first 100 metres.
Thorpe, swimming well within himself after winning the 400 freestyle world title on Sunday for a record third successive time, swam 1:47.99 in the heats and 1:47.20 in the semi-finals, winning each race.
Fellow Australian Grant Hackett, silver medallist behind Thorpe in Sunday's 400 final, was third-fastest overall in the semi-finals, clocking 1:47.72 to finish second to Van den Hoogenband.
Thorpe, who became the most prolific world champion of all time when he took his aggregate gold tally to nine on Sunday, holds the 200 freestyle world title, having avenged his Olympic defeat by consigning the Dutchman to silver at the 2001 championships in Fukuoka, Japan.