Ali released a statement calling for Pearl's safe return to his family, after the reporter's captors sent an email saying he would be executed if certain demands were not meet.
In the statement, Ali said too many people have suffered during the recent conflict and too many people had fallen victim to injustice and intolerance.
"Daniel should not become another victim of the ongoing conflict. I appeal to you to show Daniel Pearl compassion and kindness," he said.
Pearl is being held by a group which wants all the Pakistanis detained by the US in the Afghan war to be freed. As well as threatening to kill Pearl, it has warned all American journalists to leave the country within three days.
The group, calling itself the National Movement for the Restoration of Pakistani Sovereignty, accuses Pearl of working for the Israeli intelligence service Mossad. The Bombay-based Pearl is thought to have travelled to Karachi last week to write a story on Islamic militants.
The Wall Street Journal has also issued a plea for Pearl's life. It said "no good of any kind will result from the execution of Danny Pearl".
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