The Polish rider did not take to the start of stage 9 on Sunday, with his team pulling him out for "safety reasons and further examinations".
Marczynsky, 37, was diagnosed with COVID-19 in December, a Lotto Soudal spokesperson confirmed to Cyclingnews on Sunday.
He does not have a current infection and was negative for the virus in pre-race testing and follow-ups earlier this week. However, it is relatively common for COVID-19 sufferers to experience associated symptoms for several months, which has become known as 'long' COVID.
"Tomasz is struggling with post covid neurologic symptoms: headache, insomnia, dizziness and coordination problems," read a statement from Lotto Soudal on Sunday.
"Team doctor Maarten Meirhaeghe decided to pull him out for safety reasons and further examinations."
Marczynski made a late start to the 2021 season after his infection in December, riding Strade Bianche but failing to finish. He went on to complete the Volta a Catalunya but abandoned the subsequent Itzulia Basque Country on the final day. His Ardennes Classics campaign started out with two more DNFs at Brabantse Pijl and Amstel Gold Race but he finished La Flèche Wallonne and Liège-Bastogne-Liège, where he finished 91st.
Marczynski finished towards the back of the bunch on all eight stages he raced at the Giro, although his team enjoyed success in the form of two stage wins with Caleb Ewan.
"I'm sad to quit and leave my teammates, in the same time I'm really grateful to my team for supporting me in this moment," Marczynski said. "Hope to be back in few weeks."
The abandon reduces Lotto Soudal to six riders after Ewan left the race with knee pain on Saturday.
A number of professional riders have suffered with COVID-19 since the pandemic began but there have been few reports of long-term suffering. Jens Keukeleire (EF-Nippo) underwent testing as he felt his lungs weren't at full capacity this spring, but the Belgian rider is still in the Giro peloton.
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