The Serie A side have secured the services of the versatile Brazilian permanently after he impressed during a loan spell in Italy
The 25-year-old already made the move to the Stadio Olimpico side in the January transfer window on a six-month loan deal, and has now inked a contract that will keep him at Roma until the summer of 2016.
Roma will pay Marquinho's transfer fee in two installments of €2m and €1.5m respectively, with the second term to be paid before July 10, 2013.
Marquinho netted three times in 15 Serie A appearances for Roma in the 2011-12 campaign.
The Brazilian started his professional career at Palmeiras, and also wore the jerseys of Botafogo and Figueirense before joining Fluminense in 2009.