The 'Blurred Lines' hitmaker and 'Baggage Claim' actress, 37, are parents to son Julian, 3.
"We will always love each other and be best friends. However, we have mutually decided to separate at this time," the estranged spouses said in a joint statement.
Though they recently defended their marriage following Thicke's raunchy performance with Miley Cyrus at the VMAs back in August, the couple have been discussing breaking up for a long time, reported Us magazine.
Thicke, 36, also made headlines at the time for a report claiming he cheated on Patton during an August 25 party.