Details weren't immediately available, however, the ex-couple have continually sought a shared custody arrangement over children Ava, 8, and Deacon, 4.
The documents, dated June 12, only read: "[The court finds] the parties have settled all their remaining issues in these proceedings."
Witherspoon is currently dating Jake Gyllenhaal, while Phillippe, 33, recently stepped out with Australian actress Abbie Cornish, 25.
After seven years of marriage, Witherspoon, 32, filed for divorce in November 2006, citing irreconcilable differences.
The couple first met when a mutual friend brought Phillippe to Witherspoon's 21st-birthday party. Two years later, after they had costarred in 1999's Cruel Intentions, he proposed.
They married in June 1999 and had Ava three months later.
Rep for Witherspoon and Phillippe weren't immediately available for comment.