Maradona, widely considered to be one of football’s greatest ever players, died from a heart attack last month aged 60.
He holds a God-like status in the southern Italian city after spending seven memorable years playing for the Serie A club.
Naples Mayor Luigi de Magistris confirmed the renaming of the stadium in the Argentine’s honour on Friday.
It will now be known as the Diego Armando Maradona Stadium.
“The people want it; they spoke unanimously,” de Magistris said.
Napoli owner Aurelio De Laurentiis previously said in a statement: “I believe it is right to name the San Paolo after you, so we can keep you with us as a witness of the excellent path this team has taken.”
Maradona led Napoli to the club’s first Serie A title in 1987 and a second in 1990.
He was made an honorary citizen of Naples in 2017.
Murals of the Argentine still adorn walls across the city.
Argentine authorities raided the home and office of Maradona's psychiatrist Agustina Cosachov on Tuesday as part of ongoing investigations into possible manslaughter.
No one has been officially charged in relation to Maradona’s death, although many are being investigated, including Cosachov.