Madonna and John were both nominated for best original song, and Madonna took home the trophy for her song "Masterpiece," featured in her film "W.E." Her win was a surprise to many people, especially John.
Before the show, he told a red carpet correspondent that Madonna didn't have a chance at winning.
During the pop star's acceptance speech, the camera cut away to John, who didn't look pleased that she won. Later, John's husband David Furnish vented via his Facebook page.
"Madonna winning Best Original song truly shows how these awards have nothing to do with merit," Furnish wrote on Facebook. "Her acceptance speech was embarrassing in its narcissism."
Backstage after her win, Madonna was asked how it felt to beat John.
"I hope he speaks to me for the next couple of years. He's known to get mad at me," Madonna said. "He's brilliant, and I adore him ... he'll win another award. I don't feel bad."
Madonna is expected to perform at the Super Bowl half-time performance.
Will the rivalry continue for the Oscars? We'll find out when nominations are announced next Tuesday.