Clark, Australia's leading wicket-taker in the Ashes series against England, was left out in favour of the faster Shaun Tait.
"I am very disappointed but understand why the selectors have not selected me," Clark said in a statement.
"It just means I am going to have to work on my game in the next six months so that I place myself in the best possible position to be selected in the future and wish the boys the very best in defending and bringing home the World Cup for Australia."
Ponting said Clark was "desperately unlucky" not to be included, adding that there was always a chance he could play in the tournament in the West Indies starting next month.
"As we know it only takes an injury," Ponting told reporters. "Who knows, one of the guys might roll their ankle on a ball when we first arrive. I'm sure Stuey will be the first to be called up then.
"With an event that lasts for two months there's every chance that some injuries can be picked up along the way."
Ponting reiterated that Clark was not just seen as a Test specialist.
"We know what good form he has been in in the longer form of the game. We saw that right through the Test summer. He's desperately unlucky not to be in our squad.
"His Test record is outstanding. Since the moment he debuted in South Africa he hasn't put a foot wrong in the Test game. Hopefully, the selectors will explain everything properly to him and give him some exact reasons why he was left out of the squad."
