The airline is set to be fined after being found guilty last year of breaching workplace health and safety laws, facing a maximum penalty of $500,000.
Theo Seremetidis, a trained health and safety representative, was stood down in February 2020, hours after he directed others to cease cleaning and servicing planes over concerns they could be at risk of contracting the virus.
The direction came the day after the federal government closed its borders to direct flights from China.
Qantas was found guilty of breaching workplace health and safety laws. (Joel Carrett/AAP PHOTOS)
A NSW District Court hearing was told on Wednesday that Qantas had agreed to pay Mr Seremetidis $6000 for his economic loss and a further $15,000 for "hurt and humiliation".
The court will deliver a decision on Qantas's full liability in fines, compensation and costs on March 6.
It is the first instance where a major airline has faced criminal prosecution for violations of workplace safety regulations.
Outside court, Mr Seremetidis said the four-year legal battle had never been about financial compensation, but he hoped the case would act as a deterrent for other businesses.
"For me it was more about safety in the workplace and fairness," he said.
Transport Workers Union national secretary Michael Kaine dubbed Mr Seremetidis a "workplace hero".
"This is an important moment in holding Qantas to account for its illegal behaviour, its disregard for workers' safety concerns during the pandemic and its treatment of workers at large," he said.
TWU national secretary Michael Kaine (centre) says Theo Seremetidis is a "workplace hero". (Dean Lewins/AAP PHOTOS)
Mr Seremetidis directed workers not to clean the planes under Section 85 of the Work Health and Safety Act, which sets out the right of workers to cease unsafe work.
The court was told the decision to stand down Mr Seremetidis went to the "upper echelons" of primary defendant Qantas Ground Services and parent company Qantas.
Prosecution barrister Matthew Moir argued Qantas gave priority to its commercial and operational interests over the health and safety of its workers.
Qantas's lawyer, Bruce Hodgkinson, argued the airline had been attempting to deal in an educated and informed way with the unfolding pandemic.
There was "wide-ranging and very different opinion as to what was happening, and what may happen", he said.
"That applied to the workers. It applied to the managers."
Mr Hodgkinson also argued that had Mr Seremetidis consulted with management prior to making his direction, as was required under health and safety laws, the outcome might have been different.
Mr Kaine said the prosecution was the first of its kind but far from the airline's first offence, pointing to Qantas's High Court loss over the illegal outsourcing of ground staff and other cases.
Qantas acknowledged the impact the incident had on Mr Seremetidis and apologised to him.
"Safety has always been our number-one priority and we continue to encourage our employees to report safety-related matters," the company said in a statement.
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