After being freed from a prison in western France at 5.30am, Beghal, who has been stripped of his French nationality, was put on a plane for the country of his birth at Paris Charles De Gaulle airport at 10.30am, police sources said.
The 52-year-old was released 20 days early after the French authorities had spent several week discussing his repatriation with the Algerian authorities.
He had served his second sentence in solitary confinement and had spent a total of 17 years in French jails.
"Ten years ago we blocked his deportation to Algeria because of the risk of torture involved," his lawyer Bérenger Tourné told the AFP news agency. "The climate seem to him to have calmed down a great deal."
Paris rail station attack
Beghal was sentenced in 2010 for planning the escape of Smaïn Aït Ali Belkacem, a former member of the Armed Islamic Group of Algeria (GIA) who was jailed for life for the 1995 bomb blast on the regional railway network in the heart of Paris that killed eight people and wounded 117.
The escape plot had been hatched while he was under house arrest awaiting deportation in a village in central France.
Among his visitors there were Chérif Kouachi and Amédy Coulibaly, who, along with Chérif's brother Saïd, carried out the January 2015 attacks on the offices of Charlie Hebdo magazine and a kosher supermarket.
Beghal had made their acquaintance while serving a previous prison sentence for trying to set up an al Qaeda cell in France with the intention of bombing the US embassy and American cultural centres.
He acquired a reputation among young Islamists for his alleged religious knowledge and investigators considered Kouachi and Coulibaly to be his pupils.
Lived in UK
Beghal came to France at the age of 21 to study computers and married a Frenchwoman, Sylvie Guéguen, who converted to Islam and with whom he had four children.
He was first arrested in 1994 as part of an operation against alleged GIA members.
He was released without charge after four months and moved to the British city of Leicester.
In 2000 he went to an al Qaeda training camp in Afghanistan and was arrested after descending from a flight from Pakistan in Abu Dhabi in 2001.
There he confessed to the embassy bomb plot and was extradited to France.
He repeated his confession there at first but later retracted, claiming it was made under duress.