Hamza Kashgari, was sent back to Saudi Arabia despite protests from human rights groups.
Though a Malaysian High Court judge today granted an injunction to the lawyers representing the young journalist staying his deportation, the ruling came in too late as the scribe had already been flown back.
The journalist's controversial tweet on Prophet Muhammad last week was condemned by more than 30,000 responses.
Insulting the prophet is considered blasphemous in Islam and is a crime punishable by execution in Saudi Arabia.
Kashgari fled Saudi Arabia last week and was detained upon his arrival here at the Kuala Lumpur international airport on Thursday.
He had apparently fled to Malaysia after he continued to receive threats even though he had apologised and deleted the tweet.
Though Muslim majority Malaysia does not have extradition treaty with Saudi Arabia, the two nations have strong ties.
Amnesty International feared Kashgari could be executed in Saudi Arabia if he was found guilty of apostasy.
He was handed over to Saudi officials and flown back this morning.
Flight arrangements were handled by the Saudi authorities, a spokesman said.