The Home Office said Qatada's wife and children had formally dropped their bid to stay in the UK.
The move comes after the Government finally deported the extremist to Jordan following a decade-long legal battle that cost the taxpayer millions of pounds.
The family is said to have boarded a flight to Amman, where Qatada is awaiting trial on terrorism charges.
A Home Office spokesman said: "Abu Qatada's wife and five children have now left the UK. The family has formally agreed to drop an outstanding application for Indefinite Leave to Remain."
He was first arrested in the UK in 2001 over the alleged offences in Jordan and had been fighting deportation since 2005. When his battle finally came to an end, Home Secretary Theresa May said the UK Government had been vindicated.
A court had granted an injunction preventing protests outside the family home in London.