On Tuesday, a contact of the pilot tested positive, ending Taiwan's 253-day streak without a local case.
Some public Christmas activities have since been suspended and the government has suggested people should stay at home during New Year's Eve.
Overall, Taiwan has recorded only 777 infections and seven deaths.
The pilot is thought to have contracted the coronavirus earlier in December but remained asymptomatic.
Pilots returning to the island after a flight are meant to remain in quarantine for three days but are not tested unless they show symptoms.
Unaware that he carried the virus, he continued to fly and was reportedly coughing on a flight to Taiwan from the US.
He tested positive on 20 December.
Two days later, Taiwan discovered its first domestic infection in months. Authorities traced back that the infected woman had been in contact with the pilot.
Authorities fined the man 300,000 Taiwanese dollars ($10,600, £7,900) for failing to properly declare contacts and activities to officials.
Eva Air said the pilot was fired for violating operational principles, including his failure to wear a mask in the cockpit.
Other than the woman, he is thought to have infected two of his colleagues, a pilot from Japan and one from Taiwan.
Neither authorities nor the airline have named the pilot but Eva Air said in a statement "the behaviour of an individual employee has undermined everyone's efforts at epidemic prevention" and had brought "serious damage to the company's reputation and image".
In the wake of the new case, authorities are considering toughening the Covid safety requirements for airlines.
Health authorities have traced around 170 people who had contact with the infected woman and they are either in home quarantine or being monitored for symptoms.
The shops the pilot and the woman visited have been disinfected and anyone who had also visited the store has been asked to get tested.
The company where the woman works has shut its gym, café and canteen, restricted employees from eating at their desk and banned visitors from entering its premises.
Taiwan has been one of the most successful places in the world in dealing with Covid-19, largely attributed to its early and strict border controls, a ban on foreign visitors and mandatory quarantine for all Taiwanese returning home.
The island's 23 million people have also proactively been wearing face masks, even before they were required to do so.
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December 24, 2020 at 12:11PM
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Airline fires pilot blamed for Taiwan's first Covid case in months - BBC News
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