No specific details have yet been revealed about the settlement, which comes after Katie filed for divorce from Tom after five years of marriage late last month.
Jonathan said in a statement obtained by People: "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.
"This result could not have been achieved without the hard work of my partner Gary Skoloff and our co-counsel Allan Mayefsky, Michael Mosberg and Larry Trachtenberg of Aronson Mayefsky and Sloan and Peter Walzer and Chris Melcher of Walzer & Melcher in California.
"We thank Tom's counsel for their professionalism and diligence that helped bring about this speedy resolution."
Tom and Katie both confirmed in a separate statement that they are "committed" to working on their six-year-old daughter Suri’s "best interests".
Katie and Tom's representatives, Nanci Ryder and Amanda Lundberg respectively, said in a statement: "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."
Lawyers for the couple have been in negotiations to settle issues including child custody, visitation and child support for Suri, as well as property division.