The top seed from the USA conceded successive tie breaks after winning the first set at Hertogenbosch, finally losing out 6-2, 6-7 (4), 6-7 (1).
Krunic -- who is ranked 55th -- was a set and a break down at 2-6, 2-4 but rallied and saved two further break points before narrowly taking the second set.
Vandeweghe -- a two-time former champion at the Netherlands event -- had battled through an intense quarterfinal with compatriot Alison Riske on Friday.
And she was ultimately beaten by the Serbian who booked her place in just a second career final with a dominant final tie-break success.
Flipkens is a former runner-up at Hertogenbosch losing in the 2013 final to new French Open champion Simona Halep.