Knight, 66, will remain as chairman of the company's board of directors, the company said.
Shares of Nike fell 99 cents to close at $85 on the New York Stock Exchange (search) before the news was released. In after-hours trading, the shares fell another 50 cents.
Perez, 57, has been president and chief executive of S.C. Johnson since 1996. He has worked for the consumer products company for 34 years.
"I am confident that as CEO of Nike, Inc., Bill will lead Nike's extraordinary team of people to create an even bigger and better global company," Knight said in a prepared statement.
He did not give a reason for relinquishing the titles. His resignation is effective Dec. 28.
Knight and Bill Bowerman founded Blue Ribbon Sports, Inc., which was renamed Nike in 1972. Beaverton-based Nike has grown into the world's largest shoe maker, with more than $12 billion in 2004 revenues.
Privately-held S.C. Johnson, based in Racine, Wis., had $6.5 billion in revenue last year.
"You can feel the innovative spirit that Phil and his team inspires from product design, to retail to athlete partnerships. And I'm a strong believer in 'Just Do It,'" Perez said in a statement.