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.

The rare Tyrannosaurus bataar, 7m long (23ft), was bought by an anonymous bidder for more than $1m (Â£630,000) in New York.
The sale went ahead despite protests from the Mongolian president.
Elbegdorj Tsakhia says the skeleton, unearthed in the Gobi Desert, came from Mongolia and that exporting fossils found in the country is illegal.
The auctioneers, Heritage Auctions, say the specimen was imported legally. A restraining court order in the name of the Mongolian leader was put on the sale.
Tyrannosaurus bataar is an Asian cousin of the meat-eating Tyrannosaurus rex.
The skeleton in New York is thought to be one of the most complete and well preserved ever discovered, says the BBC's Jonathan Blake in Washington.
"When it comes to dinosaurs, number one, dinosaurs in general are extremely rare. But the rarest of the dinosaurs are the carnivores, the meat eaters - the top of the food chain if you will," David Herskowitz, director of natural history at Heritage Auctions, told APTV.
"And, of all the meat eaters that are out there, the most famous are the Tyrannosaurids. They are the most desirable, but they are the most elusive. They are the most difficult to find. Even though they are so big, there are not that many of them around."
Found about seven years ago in the Gobi Desert, the T. bataar remained in storage in England.
The T. bataar was slightly smaller and had longer arms than its cousin, Mr Herskowitz said.
This is the second Tyrannosaurid to be sold at auction, says Mr Herskowitz. The first was a T. rex named Sue sold in 1997 for more than $8m.
Lawyers for the auction house say the sale did not break any US laws - but it will not be confirmed until it has been approved by a US court.

Bristol Sport Ltd, which owns the football club, wants to replace two stands to increase capacity.
The plan is an alternative to proposals to build a new stadium at nearby Ashton Vale, which has been delayed by an application for a town green.
Majority shareholder Steve Lansdown confirmed the club would begin work at a shareholder meeting on Tuesday.
The work was approved by Bristol City Council in November.
Mr Lansdown told the club's official website: "We'll sign the section 106 agreement any day now, and then we have six weeks to wait for the judicial review period.
"We wanted to give some certainty to supporters, so if we get through to March with no judicial review, then we will be going ahead with the redevelopment plans, starting in May."
Mexican President Enrique Pena Nieto has fired a senior official over an incident caused by his daughter at an exclusive restaurant last month.
[NEXT_CONCEPT]
A row has broken out over the sale of a dinosaur skeleton at auction in the US.
[NEXT_CONCEPT]
A £40m revamp of Bristol City's Ashton Gate ground will go ahead this summer, the club has announced.