The 20-year-old divorcee was executed on Tuesday after confessing to having had sex with a 29-year-old unmarried man.
Sheikh Ibrahim Abdirahman, the judge for a court created by the rebel group al-Shabab, says the woman was killed in front of a crowd of some 200 people near the town of Wajid.
The woman, who gave birth to a stillborn child, was buried up to her waist before the stoning took place. Her boyfriend was given 100 lashes for having the affair.
The woman's death is the second recorded stoning for adultery carried out by al-Shabab fighters, who are confronting the government and control large parts of Somalia.
Al-Shabab are proponents of stoning as a punishment under their interpretation of sharia (Islamic law).
Mohamed Abdullahi, an East Africa analyst, told Al Jazeera that Islamic law can only be conducted where there is proper jurisdiction in place - not in a lawless failed state like Somalia today."The position of the majority of Somalis is that these courts should not be held at all," he said.
"What they are doing is atrocious and un-Islamic, as they don't have at the moment the right investigative judicial setup necessary for such a verdict, in which capital punishment can be brought forward.
"You must have a legal system, a witness system, peace and this is the view of the Somali ulema (legal scholars), the muftis (Islamic law interpreters), that no such verdicts can be conducted in Somalia at the moment."
One man was stoned to death for adultery last week.
His pregnant girlfriend is due to be given the same punishment in the next few months after she gives birth.
In November 2008, a 13-year-old rape victim was stoned to death after being accused of adultery, according to Amnesty International, the London-based human rights group.