The interior ministry statement announcing the execution began with a verse from the Quran, according to SPA, the official Saudi News agency: "O ye who believe! the law of equality is prescribed to you in cases of murder."
The death penalty for Nafeek had been approved by the Supreme Court, the agency reported, and a "high order was issued" to carry out the sentence.
The Sri Lankan government and human rights groups have sharply criticized Saudi Arabian authorities for the beheading of Nafeek.
It shows "once more how woefully out of step they are with their international obligations regarding the use of the death penalty," said Philip Luther, director of Amnesty International's Middle East and North Africa program.