The left-sided defender, who can also play in midfield, 22, has spent most of the past five years on loan to Spanish sides, including two spells in La Liga last season, where be played for Rayo Vallecano and Levante.
The Brazilian club, who were relegated last season, announced the deal on their website, saying the player wished to return to his homeland.
“Atletico should not be in the second division,” the player said. “They have a good team and a great fanbase.
“I’ve been at Arsenal and other European clubs and the structure here is up there with the best of them.
“I’m hungry to win and help the club achieve the aim of reaching the first division.”
Botelho’s move comes after a troubled last season in Spain, where he had to leave Madrid-based Rayo due to personal problems before struggling at Levante.