Joanna Muir – a women’s relay silver-medallist with Murray at the start of the week – also fell narrowly short of qualification on her debut at the senior World Championships.
Third-placed finishes for University of Bath Politics & French graduate Murray in the fencing and swimming put her top of the rankings going into the combined event in Pool A.
She was able to cruise around the 3,200m course to finish fifth overall and comfortably progress to the final, where she will be looking to reclaim the title she won in 2014.
Prentice was in the same group and started well in the fencing but a disappointing final five rounds saw her go into the swimming ranked 23rd.
She remained in that position after the swim and, despite producing a brilliant effort in the run/shoot to set the second fastest time, Prentice could only move up to 17th.
The Biology graduate, who finished sixth at the World Cup Final two weeks ago, is still in contention for Rio via the world ranking list but knows selection is now out of her hands.
It was my head that let me down today. It changes things when you want something too much. Pentathlon is the most frustrating sport ever 😢
— Freyja Prentice (@freyjaprentice) May 25, 2016
Pentathlon GB Performance Director Jan Bartu said: “This competition was very difficult for Freyja. She needed a solid performance to cement her place on the Olympic qualification list but unfortunately couldn’t follow through her form in the fencing.
“This is what put her on course to not make the final because, despite one of her best swims this year, she was not in an effective place in the combined event to qualify.”
French – who, like Murray, holds an Olympic qualifying quota place – came home joint first in Pool B after strong performances across the four disciplines, the ride not being contested during the qualifying rounds.
Bartu said: “Both Samantha and Kate put on a good show, they made a clear passage through the semi-finals and really competed well. They can still improve for the final but it was a good day.”
Sports Performance graduate Muir narrowly missed out on a place in the individual final after dropping from tenth to 14th in the Pool C combined event, putting her 40th overall.
“Joanna found it a very testing competition,” Bartu added. “She did well from the outset, swam a PB and put in a solid fencing performance to pick up 11 victories which is good for her.
“Unfortunately she found herself in the middle of a very competitive combined event and just missed out on a place in the final.”
There are expected to be more than 100 male athletes in the three semi-final groups and Bartu said: “This will make the semi-finals very tough – I think it will be the hardest men’s competition this year.”