They were married five years and have a 6-year-old daughter, Suri.
Holmes filed for divorce June 28 in New York.
"The case has been settled and the agreement has been signed. We are thrilled for Katie and her family and are excited to watch as she embarks on the next chapter of her life," Holmes' attorney, Jonathan Wolfe, said in a statement to People.com.
"We thank Tom's counsel for their professionalism and diligence that helped bring about this speedy resolution."
Holmes and Cruise said in a joint statement through their respective representatives Nanci Ryder and Amanda Lundberg:
"We are committed to working together as parents to accomplish what is in our daughter Suri's best interests. We want to keep matters affecting our family private and express our respect for each other's commitment to each of our respective beliefs and support each other's roles as parents."