Joanne Baldwin - who has two children, Avis, three, and 23-month-old Finley, with the actor - was taken into custody in Portland, Oregon, after she turned herself in to the Lake Oswego Police Department after admitting to consuming alcohol.
She was booked and transferred to Clackamas County Jail, where she remain without bail until her court appearance on July 20.
Her arrest comes after Daniel filed for divorce, claiming she was addicted to drink and drugs, which happened just a day after he was granted a temporary restraining order against his spouse.
Daniel - who met Joanne in 2007 when she was working as a chef in the rehab facility he was receiving treatment in for drug addiction - said: "Due to recent events in our home and for the safety of my children and myself, I have made this decision.
"I have had my share of problems with drugs and alcohol many years ago and know firsthand how difficult a position she is in."