The housekeeper, who has a 13-year-old son by the actor, explained that Shriver asked if Schwarzenegger had fathered her child after noticing the increasing similarity.
Baena, who was a trusted member of the family's domestic staff, told Hello: "[Maria] was so strong. She cried with me and told me to get off my knees. We held each other and I told her it wasn't Arnie's fault. It takes two."
Baena, who was photographed for the magazine with her son for the first time, said that Shriver has been suspicious for a while.
She explained: "She would say things like, 'I'm here if you need to talk.' I sensed something was up. I have so much love and respect for Maria."
Baena, who had worked with the family for years, said that her son had been told of his parentage a year ago.
She also insisted that Schwarzenegger is a "good man" and hopes that the family will work out their issues.
She added: "He's a good man and I know he is suffering too. He loves Maria. I hope in time they work things out."
Schwarzenegger and Shriver announced their separation in May after 25 years of marriage.
They said in a statement: "We are continuing to parent our four children together. They are the light and the centre of both of our lives. We consider this a private matter and neither we nor any of our friends or family will have further comment. We ask for compassion and respect from the media and the public."