Stephen Tacchini was appointed deputy chief of field operations less than a month ago as part of a sweeping change Chief Heather Fong made in her command staff.
Chief Fong told ABC7 News she fired him from his command and demoted him as well.
"Effective on Saturday February 9th, he will be retiring to his permanent civil service rank as captain of police and because its a personal matter, its not appropriate for me to share specifics with you," said San Francisco Police Chief Heather Fong.
Tacchini's demotion comes three weeks after his son, 23-year-old rookie officer James Tacchini, was questioned by police investigating a 911 domestic violence call.
Police responded to an apartment on the 300 block of King Street where they interviewed both Tacchini and his female friend.
A lieutenant after being briefed at the scene reportedly called Tacchini's father, and a police report was never filed, although witness statements were taken.
Tacchini has come under scrutiny because of the possibility that he may have had something to do with the handling of the incident.
The case has similarities to the 2002 "Fajitagate" scandal, in which the son of Assistant Chief Alex Fagan was accused of beating up two people.
The head of the police officers union says that call to Ceputy Chief Tacchini should never have been made.
"Once that call is made, it gives the perception that something's going on and that's just not something we can afford in this report right now post "Fajitagate," said Police Officer's Association President Gary Delagnes.
Mayor Gavin Newsom stands by his chief's decision.
"I mean I think the whole incident is unfortunate and all I asked from the police chief was a fair and partial investigation of the facts and her judgment on what to do next," said San Francisco Mayor Gavin Newsom.
The department is still investigating the incident.
Tacchini, who's on a two-week leave, declined to comment because of the ongoing probe.
His demotion means a salary cut from $220,000 dollars to $163,000 a year.