Janice Linden, 35, was convicted of trying to sneak three kilograms (6.6 pounds) of methamphetamine into the country in her luggage through the southern city of Guangzhou in 2008.
“The execution took place around 10:00 am South African time (0800 GMT),” spokesman Clayson Monyela told AFP. “Our embassy officials were there with her family. She had two sisters who were there.
“We are disappointed since we would have preferred the death sentence to be commuted to a life sentence instead of the execution.”
Convicted in 2009, Linden had exhausted all possible appeal processes.
South Africa had made several appeals to have Linden’s sentence converted to life imprisonment, including on the sidelines of the United Nations COP17 climate talks in her eastern hometown, Durban, that ended Sunday.
“Even on the COP17 sidelines the (foreign) minister summoned the Chinese ambassador,” said Monyela. “We pleaded for clemency repeatedly.”
Chinese foreign ministry spokesman Liu Weimin told AFP in Beijing that the law had been followed.
“On handling drug criminals, the Chinese government’s position has been consistent and clear,” said Liu. “Whether they are foreign or Chinese, China will handle their cases according to the law.”
Chinese authorities would hand over Linden’s ashes to her family on Monday, said Monyela.
Linden steadfastly insisted on her innocence, an unnamed family member told The Mercury newspaper in Durban.
“She said she didn’t know how the drugs got into her luggage. She thought she was framed.”
Monyela denied the execution would harm relations with China, South Africa’s biggest trading partner.
The main opposition party Democratic Alliance (DA) accused South Africa of sidestepping human rights issues for commercial gain.
“In this context a reference to South Africa’s economic relationship with China seems to confirm the DA’s assertion that our foreign policy is ‘made in China’ and that where China is involved the government seems to consistently turn a blind eye towards human rights abuses,” said Stevens Mokgalapa, the party’s shadow minister for international relations, in a statement.
“Whilst we firmly believe that drug mules should be punished for their offences, this punishment does not fit the crime.”
In October, South Africa kept the Dalai Lama from visiting the country for Nobel laureate Desmond Tutu’s 80th birthday.
A government official later acknowledged the decision was influenced by fears that South Africa’s trade relations with Beijing would suffer if the Tibetan spiritual leader were allowed to visit.
Trade between the two countries reached $4.9 billion (3.7 billion euros) in the first six months of the year.
According to the rights group Amnesty International, China executes more people every year than the rest of the world combined.
Executions in China have traditionally been carried out by shooting. But increasingly lethal injections are being used.