Samuel Oliver-Bruno, 47, was removed from the US and taken to Mexico, according to US Immigration and Customs Enforcement (ICE) spokesman Bryan Cox.
Mr Oliver-Bruno was arrested on November 23 at an immigration office near Raleigh after he left the church to have his fingerprints taken as part of an application to stay in the US to financially support his son and ailing wife.
His application to stay in the US was denied earlier this week.
He had been living in the Durham church since late 2017 to avoid immigration officers, who generally do not make arrests in churches and other sensitive locations.
Plainclothes officers detained him when he entered the Morrisville office of US Citizenship and Immigration Services last week.
Outside the office, more than two dozen of his supporters were arrested on misdemeanour charges including resisting officers, after some of them blocked the van being used to drive Mr Oliver-Bruno away.
ICE previously said Mr Oliver-Bruno, who has lived in the US for two decades, had no legal basis to be in the country.
He pleaded guilty in 2014 to using false documents to try to re-enter the US in Texas after a trip outside the country, according to court records.
Since his arrest, his supporters have held rallies and organised a campaign to lobby elected officials and the US Government to reverse its decision.
Democratic US Congressmen David Price and GK Butterfield, both of North Carolina, had urged Homeland Security to release him, calling his treatment unacceptable.