"It sounds like it was a wonderful wedding. It must have been very beautiful with the kids participating. I know it was during Emmy weeks and they were able to do it very quietly," Jon told E! News in a statement.
"I'm very happy for them," he concluded.
The actor, 75, was not present when the Hollywood couple tied the knot last Saturday in France, but sources revealed to Just Jared that Jon was invited to the nuptials.
Angelina and father Jon had been estranged for years before making up in 2010, when they were pictured together with the actress's children.
Speaking about their reunion at the time, Jon said: "We're in touch, but not regularly," he said. "We love each other and that's the most important thing."