They were ordered down by a Belfast court on Friday, after they carried death threats against a Catholic man.
His lawyer had been critical of the length of time it took the social media giant to act.
He had threatened to take further legal action if they were not removed by 09:00 GMT on Tuesday.
The sites were Loyalists against Short Strand and Loyalist Peaceful Protests Updater.
The sites had provided information about street protests being held in Northern Ireland.
They have been ongoing since a decision was taken by councillors on 3 December to limit the number of days the union flag flies at Belfast City Hall.
In his ruling at Belfast High Court, the judge ordered that the man's picture and details about him should be prevented from appearing on any other web pages controlled by Facebook.
The flag dispute is now in its seventh week.
Some of the protests have been followed by rioting in which more than 100 police officers have been injured.
Two Facebook sites related to the loyalist flag protests have been removed.