The couple's relationship first crumbled in 2008, when they separated and The X-Files star underwent therapy for sex addiction.
They subsequently reunited and split several more times over the last few years, and were recently rumoured to be giving the marriage another shot.
However, it has now emerged the union is over for good. Duchovny filed for divorce in June (14), citing an irretrievable breakdown of the relationship, and editors at Tmz.com report the split has now been made official after a settlement was reached.
Leoni is reported to have primary physical custody of their two children, aged 15 and 12, but the stars share joint legal custody of the kids. Duchovny is believed to be paying just over $8,000 (£4,706) a month in child support, plus around $40,000 (£23,529) in spousal support.
The former couple married in 1997.