Jones had led 4-0 in the decider before suffering with a bout of cramp that left her needing to be helped off court.
The 23-year-old lost the first set but rallied to win the second in a tie-break before taking charge and breaking Seidel twice to close in on a place in the final round of qualifying.
Jones called for the physio at 4-2 but with players unable to call a timeout for cramp, the problem persisted and got worse.
She was docked a point with Seidel serving at 4-3 because she wasn’t ready and retired at the end of the next game with the set poised at 4-4.
There was more disappointment for British hopefuls, as Harriet Dart, Ryan Peniston and Billy Harris all lost, although Oliver Crawford progressed with a 6-4 6-7(7) 6-4 win over Italy’s Francesco Passaro.
He will take on Vit Kopriva for a place in the main draw.
Raducanu allays injury fears
She admitted she felt soreness following her second-round loss in Auckland to Elina Svitolina on her comeback from wrist and ankle surgeries in May of last year.
However, she looked back to full fitness as she hit the practice court ahead of her first-round encounter against American Shelby Rogers.
Elsewhere, men’s British No. 1 Cameron Norrie pulled out of an ATP event in Auckland with a wrist injury, although he is expected to be fine for his opening match of the Australian Open against Peru’s Juan Pablo Varillas.
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