The two-story contemporary home had been put up for sale in June at $4.79 million.
Designed by Marmol Radziner, the home sits on 1.36 acres with a free-form pool and an outdoor fireplace.
There are three bedrooms, three bathrooms and an office in more than 3,000 square feet.
Flea - real name Michael Balzary - bought the previous house on the site in 2002 for $2.55 million but it burned down in the 2007 Malibu fires.
The musician owns another house in Malibu that was purchased in 2006 for $9.98 million.
Flea, 49, is a founding member of the Grammy-winning band, whose 10th album I'm With You was released recently.