Humberto Benitez Trevino's daughter caused outrage by using his influence to try to close down the bistro after it did not give her a table she wanted.
The episode sparked a discussion about abuse of power in the country.
The sacking suggests that Mexico has grown more sensitive to the issue, correspondents say.
The episode became a trending topic on Twitter under the hashtag #ladyprofeco, after her father's agency.
Mt Benitez, the attorney-general for consumer protection, and his daughter both apologised, but this did little to appease public anger.
On Wednesday, President Pena Nieto ordered his dismissal.
The restaurant, Maximo Bistro in Mexico City, was raided by officials after Andrea Benitez was not offered the table she had asked for.
The government said that although Mr Benitez was not personally involved in the raid, the episode had become embarrassing for the institution.
Mexican President Enrique Pena Nieto has fired a senior official over an incident caused by his daughter at an exclusive restaurant last month.