The 31-year-old striker is handing over his jersey as part of a Museum of London plan for future generations to witness how the pandemic changed lives.
The project will also reflect the Black Lives Matter protests, which took place earlier this year.
Aubameyang said: “I am proud to be the latest black player to captain Arsenal and it’s an honour to have the opportunity to donate my Black Lives Matter shirt to the Museum of London’s Collecting Covid project.
“I hope this will be remembered as the moment that football stood against all forms of racism and that it will inspire young people for the future.”
The Black Lives Matter logo was added to Premier League shirts following anti-racism protests, sparked by the killing of George Floyd in the US.
But shirts now feature a patch with the league’s own anti-racism campaign, No Room For Racism, following controversy over the Black Lives Matter organisation.
The Museum of London tells the story of the city and its residents from 450,000BC to the present.
There are no confirmed plans for a Collecting Covid exhibition, so the shirt will not go on display immediately.
But it is part of plans to collect objects – which could include anything from a video clip of Joe Wicks helping pupils keep fit, to clippers used when hairdressers were closed – to reflect how coronavirus changed society.
Foteini Aravani, the museum’s digital curator, said: “We are very excited about the generous offer from the captain of Arsenal, Pierre-Emerick Aubameyang.
“This jersey, part of Arsenal’s Black Lives Matter tribute kit, will be a very important addition to the growing number of objects the Museum of London is acquiring as part of our Collecting Covid project.”
The jersey is “an important reflection and response to Black Lives Matter as a movement and its resonance through London and its people”, she added.
