Her two sons, now aged 22 and 37, were allowed to stay at about the same time. Another son of Rifaat who has a different mother was granted indefinite leave to remain in 2014.
Rifaat has four wives and is thought to still be married to all of them. He fell out of favour with his brother Hafez, Bashar al-Assad's father, after a failed coup in the 1980s that led to his exile.
Details of the case are contained in a 37-page ruling by the Special Immigration Appeals Commission (SIAC). Under its rules, the woman and children cannot be named. The family had appealed after being denied British citizenship. The court rejected their claim.
The woman, known in the ruling only as "LA", is, according to the judgment, the fourth wife of Rifaat al-Assad.
According to the ruling, his wife first came to the UK in 2006 and was given "entry clearance as an investor" after she told the Home Office that she was "investing in bonds, hedge funds etc".
A number of relatives of President Assad and his British-born wife Asma live in the UK, including her father Fawaz Akhras, a cardiologist.
Rifaat al-Assad gained the nickname the "Butcher of Hama" after leading an elite force that put down a Muslim Brotherhood insurrection in Hama in 1982, a crackdown that claimed between 10,000 and 40,000 lives.
Human Rights Watch reported that he was responsible for the massacre of more than 1000 prisoners in the notorious Tadmur jail in 1980.
He owns a £10 million Georgian mansion off Park Lane, central London and has houses in London, Marbella and France.
According to the SIAC ruling, the Home Office told the wife: "You are the wife of Rifaat al-Assad the uncle of President Bashar Al-Assad of Syria. Although widely reported as estranged from Bashar Al-Assad, Rifaat was a prominent member of his brother's regime during the Seventies and Eighties - a regime that is widely held to have committed crimes against humanity."
The Home Office concluded that to grant the family citizenship would have an adverse impact on the UK's international relations and would not be in the public interest.