Johnson and Kelly came out on top after six skills events and the unusual reverse scramble format at The Breakers.
Kelly and Johnson both converted six-foot par putts after Nick Price missed a five-footer of his own. Those pars gave the PGA duo $200,000 of the $286,000 they will split for winning the event.
"It comes down to putting, which is exactly what golf is," said Johnson. "We understood that we both were going to have to make a putt. The format's unique and it's nice to incorporate golf into the skills competition and there's nothing better than playing as a team."
It was the first time there was an all-women's team competing. Morgan Pressel was paired with Hall-of-Famer Annika Sorenstam, who played an event for the first time since retiring at the end of the 2008 season. They finished fourth with $161,000.
Faldo and Mediate won three of the first six skills, while Sorenstam claimed the short iron challenge. Pressel bested Price in a playoff to win the bunker competition after both players holed their first shot and the PGA team won the putting challenge.