The winger has put pen to paper on a two-year deal with the Rams, with the option of a further year, after turning down the offer of a new contract with the Pirates following their relegation from the Football League last season.
Santos attracted interest from several clubs and had been offered the chance to play in the Premier League, with Hull thought to be the club interested in signing the 19-year-old. But after holding discussions with Derby, the Brazilian has joined Steve McClaren's men.
"We are pleased to welcome Alefe to Derby County," said Rams head coach McClaren.
"He is a player with potential and has the determination to improve, so we are looking forward to working with him."
Santos was born in Sao Paulo and moved to England at the age of 12. He started his football career as a schoolboy at Bristol Rovers and went on to progress through the youth system at the Memorial Stadium, before signing his first professional contract in 2013.
He made 27 appearances last term and scored his first-ever professional goal in a 1-1 draw at Mansfield in October.