Ms Varnhagen's legal team applied to the Supreme Court to require Professor Nicola Spurrier to give evidence about what information she relied on in her role advising the state emergency coordinator during the COVID-19 pandemic.
Lawyers for the Adelaide Crows midfielder told the court the application was not an effort to grandstand or "turn the court into some kind of royal commission" and said any cross examination would be conducted with "the utmost courtesy".
Government lawyers argued an application requiring her to give evidence should not be allowed as it was taking place against her will and would not add any additional expert evidence.
Justice Judy Hughes rejected the application on Thursday.
"I've determined there is no relevant evidence that Prof Spurrier can give on the grounds that have been asserted," she said.
Justice Hughes said reasons for the decision would be provided at a later date.
It remains unclear whether SA Police Commissioner Grant Stevens will also be required to give evidence.
In the lead up to the trial, Ms Varnhagen's legal team issued Prof Spurrier with a subpoena which required her to attend court on Thursday morning.
A group bearing signs with anti-vaccine messages gathered at the entrance to the District Court building in Adelaide, where they shouted "shame" and called for Prof Spurrier to be prosecuted as she entered the building.
The legal case is challenging the state's vaccine requirements for healthcare workers.
Ms Varnhagen, who is also a nurse, has had to work as a labourer after losing her regular employment for refusing a COVID-19 vaccination, the court was told.
The decision to impose the vaccination mandate for state health workers and other public sector employers was made under the SA Emergency Management Act.
Ms Varnhagan says she has received no nursing shifts since November 2021 after refusing vaccination despite receiving text messages asking for all eligible nursing staff to help fill shortages.
The Crows also shifted Ms Varnhagen to the inactive list after she refused to be vaccinated.
Ms Varnhagen has been joined in the matter by several other people.