Earlier this month, a London court said Mr Zakayev would not get a fair trial in Russia, and could even face torture.
Russia claimed he was a rebel soldier responsible for kidnap, killing Russian soldiers and levying war.
The Home Office said on Saturday: "We can confirm that Mr Zakayev has been granted refugee status."
Star backer
Supporters, including the actress Vanessa Redgrave, who stood surety for 」50,000 bail last December, claimed Mr Zakayev had been "demonised" by Russia.
Thirteen allegations against him relate to incidents between October 1995 and December 2000, when Chechnya was fighting for independence.
One witness at Bow Street Magistrates Court in June told the hearing how the Russian foreign minister Igor Ivanov had publicly compared Mr Zakayev to Osama bin Laden.
Mr Zakayev denied all the charges.
Mr Zakayev has acted as a representative of Aslan Maskhadov, the rebel leader who considers himself president of Chechnya.
A pro-Moscow candidate, Akhmed Kadyrov, was elected Chechen president in an October vote that was condemned by observers and rejected by the rebels.
