Ghannouchi said 12 ministers were replaced, stressing the government was in "transition," the BBC reported.
Tunisians maintained their protests, despite the Cabinet shuffle and a pledge by Ghannouchi that the government would "take the country to democracy."
Anti-government rallies were staged Thursday in Tunis and Sidi Bouzid.
Ghannouchi announced the changes to the 22-member Cabinet Thursday, with only two ministers from the Ben Ali regime remaining and other posts filled by independents, the North African Journal said.
The changes was welcomed by the Union Generale des Travailleurs Tunisiens labor union, although it said it would not join the new government, the BBC reported.
Observers contended the presence of Ghannouchi, prime minister for Ben Ali for years, was necessary to ensure the transition was as smooth as possible with the approval of the powerful labor union, the Journal said.
Ghannouchi promised to step aside "in the shortest possible time frame" and to conduct elections within six months, the BBC said.
Tunisia issued an international arrest warrant Wednesday for Ben Ali, who fled to Saudi Arabia Jan. 14, the BBC said. He is accused of illegally acquiring property and assets and moving funds abroad while he was president.