The 19-year-old defender completed a medical on Monday and has now finalised a €10 million switch to the Ligue 1 club
The highly-rated 19-year-old centre back has been persistently linked with a move to Europe this summer and speculation has increased with Botafogo in the midst of a financial crisis that has seen a number of players go without wages.
After completing a medical on Monday, Doria admitted he was delighted to be joining a European side with the pedigree of Marcelo Bielsa's outfit.
"I'm very happy, honoured and proud to join Marseille," he told the club's official website.
"This is one of the biggest clubs in Europe, well known in Brazil.
"I am fully prepared and trained with Botafogo before I signed with Marseille. I'm in great shape, ready to play.
"I've heard of the passion fans of Marseille. I know they play a very important role. I saw pictures from the Stade Velodrome in the last game of Marseille against Nice, it was amazing."
Botafogo boss Vagner Mancini said the stopper, who was also attracting major interest from Lyon, Lazio and Valencia, will be sorely missed by the Rio de Janeiro club.
"He's a spectacular athlete, he's so much more than everybody thinks," Mancini told a press conference on Sunday.
"He'll be soon be playing for Brazil. I am sorry he's leaving, we'll miss him very much. He's an unique talent. I wish him luck for his future career."
The under-20 international has made one appearance for the senior national team, appearing against Bolivia last year in a friendly for domestic-based players only.
He will cost the Ligue 1 club a fee in the region of €10 million, of which around Botafogo will receive €3 million for the 30 per cent stake they hold in his registration.