The club's website said in a statement on Sunday. Costa will serve as president until 2025.
He got 84.48 percent votes. Opposing him, Francisco Benitez received only 12.24 percent of the vote.
The club said that slightly more than 40,000 of its members voted, a record turnout.
Costa, 49, began his professional career in Benfica. After that he played for two Italian clubs AC Milan and Fiorentina for 12 years. The scale of his success for the San Siro club was even heavier. For Milan, Serie A has won several major titles, including the Champions League.
Costa picked up the pair of boots two years after returning to the Portuguese club in 2006.
The midfielder has scored 23 goals in 92 appearances since making his debut for Portugal in 1993. He retired from the national team in 2004 after a 1-0 defeat at home in the European Championship final against Greece.