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Records filed in a New York City court indicate the case was formally closed on Monday.
Katie and Tom said in July they had reached an agreement less than two weeks into their headline-dominating divorce case.
Their lawyers and representatives would not disclose details, but it's thought Katie was awarded full custody of the couple's six-year-old daughter Suri - with generous visitation rights for Tom.
Katie's layer Jonathan Wolfe said back in July: "We are thrilled for Katie and her family and are excited to watch as she embarks on the next chapter of her life.
"We thank Tom's counsel for their professionalism and diligence that helped bring about this speedy resolution".
The Top Gun star's lawyer, Bert Fields, added: "Tom is really pleased we got there, and so am I."
Shockwaves were sent through the celebrity world in June when Katie filed for divorce after five years of marriage.
The Top Gun actor, 50, married Dawson's Creek star Katie, 33, in a magnificent Italian castle ceremony in November 2006, seven months after the birth of their daughter.
Tom was previously married to Moulin Rouge star Nicole Kidman, with whom he has two children, and actress Mimi Rogers. It was Katie's first marriage.