The Northern Irishman leapfrogged Luke Donald after finishing second to Rickie Fowler in the first extra hole, in which American DA Points was also competing.
It is the fifth time since the start of March that the British pair have swapped places at the top of the world rankings. Donald's latest tenure at the summit lasted just one week.
"It's a little consolation," said the 23-year-old. "I would rather win the tournament, but it's good.
"I want to try to play well for the next few weeks and solidify my spot at number one."
McIlroy regained the number one spot on the same course where he claimed his first ever Tour win two years ago.