After their individual battles against the clock over 32.3 kilometres of undulating, damp terrain around the Glasgow streets, only two seconds could separate the triple champion Van Dijk from her team mate.
It was so close that when she crossed the line, Van Dijk originally thought she had just missed the target time of 41 minutes and 41 seconds earlier set by Olympic road race champion Van der Breggen.
"I thought first that Anna had won by two seconds but then I heard it was me," said the 31-year-old Van Dijk, whose official winning time was 41:39.
"So it was super, super close especially after such a long time trial and I'm really happy to be on the good side."
The Dutch pair, making amends for their team's failure to win the road race title at the weekend, were in a different class to their opponents, with German bronze medallist Trixi Worrack (42:48) well over a minute behind.
Van Dijk, the world time trial champion two years ago and formerly a global champion on the track as well as the road, had looked in control as she led by 17 seconds at the halfway stage as the race had already become a two-rider duel.
"But it was challenging with wet roads and a slippery course rolling up and down and at the end it was very tricky," said Van Dijk, whose lead was eaten into on the ride back towards the city centre.
For the 28-year-old "Queen of the Ardennes" Van der Breggen, who has enjoyed a superb year, it was, frustratingly, the second successive year that she had finished behind Van Dijk in this race, claiming bronze in the 2017 edition.
The men's time trial was scheduled for later on Wednesday.