Tati Tursilawati, a mother, was executed in the western Saudi city of Taif on Monday.
In a breach of international protocol, the execution took place without either Ms Tursilawati’s family or the Indonesian government being informed in advance.
Ms Tursilawati was sentenced to death seven years ago for killing her employer.
She claimed she was acting in self-defence after he attempted to rape her.
The decision was furiously condemned by Indonesian president Joko Widodo who said: “We have called Saudi Arabia’s foreign minister and conveyed our protest.”
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Lalu Muhammad Iqbal, director of the Indonesian foreign ministry’s citizens protection department, commented: “The execution of Tuti Tursilawati was done without notification to our representatives, either in Riyadh or Jeddah.”
He described the execution as “regrettable” – the diplomatic language tended to be used when a country is angry at a decision.
There is ongoing controversy over the treatment of migrant workers in Saudi Arabia and other Gulf Arab states.
In 2015 Indonesia banned its nationals from working as domestic workers in Saudi Arabia after two Indonesian maids were executed in the same year, though this has since been reversed.
Migrant Care, a charity which campaigns to improve the treatment of Indonesian immigrants, is calling for the ban to be reimposed.
Ms Tursilawati is the fourth Indonesian worker executed by the Saudis over the past three years, all without prior notice being given.
Another 18 Indonesians remain on death row in the country.
The Saudi government is facing intense international pressure over the death of dissident journalist Jamal Khashoggi in the country’s Istanbul consulate on October 2.
Turkish authorities claim Mr Khashoggi was murdered and dismembered by a Saudi hit squad.
Turkish chief prosecutor Irfan Fidan stated: “Jamal Khashoggi was choked to death immediately after entering the Consulate General of Saudi Arabia.”
He added the murder took place “in line with advance plans”.
The Saudis initially claimed Mr Khashoggi left the consulate alive, but now say he was killed during an altercation with a rogue Saudi unit.
President Trump described the aftermath of Mr Khashoggi as “the worst cover-up ever”.
The Saudi government is yet to produce Mr Khashoggi’s body.