Clarke was ruled out on Tuesday after scans revealed the hamstring injury that cut short his Zimbabwe tour was worse than first thought and included tendon damage.
The national selection panel confirmed Hughes will replace him in the three-game series in the United Arab Emirates.
Hughes had been named in the Test squad to play Pakistan and was set to travel to the UAE earlier than his teammates to work on his batting against spin with coaching consultant and Sri Lankan great Muttiah Muralitharan.
The three-game one-day series against Pakistan, the last for Australia before it hosts the World Cup next year, starts on October 7 with the first of two Tests not until October 22.
Cricket Australia said Tuesday it hoped that Clarke, who has a history of back and hamstring trouble, would be fit to play in the first Test.
Pakistan have been forced to play their home series at neutral venues, such as the UAE, since militants attacked the Sri Lankan team in Lahore in 2009.