Joseph (Wellington) made a strong start from 24th, moving up four places in the starting loop and was 17th after lap one. She edged back to 22nd on lap two and stayed there for the rest of the race, finishing 5m 26s back.
"I'm feeling disappointed with my race," said Joseph. "I really liked the track, and I think it suited me well with the steep climbs and technical descents.
"I had a pretty good start and was in decent position but just didn't have the spark needed to have a great race. A slow leak in my front tyre slowed me down for a bit too.
"But I tried hard and am feeling spent now, so I guess I couldn't have done much more."
It was the first time Joseph has bettered Hanlen this year as they battle for Olympic selection.
The Whakatane rider won the domestic national series and finished ahead in the world cup's first two rounds, with eighth in South Africa and 18th in Belgium.
Hanlen had her problems on the starting loop, despite her front draw, after being held up with a crash on the first lap and then with mechanical issues.
She fell back to 44th at the end of the first lap. The 32-year-old, who rode splendidly for runner-up in the BMC Swiss Cup last week to finish ahead of the likes of Bresset and Kalentieva, gradually worked her way through the field to finish 26th, more than a minute behind Joseph.