Lyon -- who has taken 247 wickets in 67 Tests -- replaces pace bowling compatriot John Hastings who will compete in the 50-over tournament from June 1-18.
"Nathan has been mainly playing Test cricket for Australia and is available for Worcestershire as he has not been picked for the Champions Trophy, Australia having selected a couple of batting spinners instead," said Director of cricket, Steve Rhodes.
"He is the number one international spinner in Australia at the moment and just had recent success in India.
"He is a very good replacement. It is a different slant, from a pace bowler to a spin bowler.