Only male singers including Ricky Martin have previously achieved the feat in the chart, which began in 1986.
Estefan has sold 90 million albums during her five-decade career.
The Cuban-American singer came to prominence performing with the Miami Sound Machine in the late 1970s.
She went on to score a series of hit albums and singles, including Don't Wanna Lose You which was a number one hit on the mainstream US chart in 1989.
Estefan has collected seven Grammy awards and in 2008 was honoured with a special Latin Grammy award for her musical achievements.
The singer's breakthrough success on the Latin chart is being attributed to very strong airplay on a leading group of Spanish language radio stations in the US.
The song, with its mixture of Spanish and English lyrics, is Estefan's 15th chart-topper on Billboard's Latin countdown.
It becomes only the 11th song since 1986 to debut the chart in the top spot.