The Brazilian was pictured holding a Lyon shirt alongside director of football Juninho in images uploaded to Twitter by club president Jean-Michel Aulas.
The official Lyon account replied to the tweet, commenting: "Announce Guimaraes".
Arsenal, Atletico Madrid and Benfica had been linked to the 22-year-old, who won the Copa Sudamericana in 2018.
Juninho reportedly travelled to Colombia, where Guimaraes is involved in Olympic Games qualifying with Brazil, to seal the deal.
He will become part of Rudi Garcia's squad at Lyon, who sit fifth in Ligue 1 after 21 games.