Amid the drama, the pastor, from a Durban church, was arrested on human trafficking charges.
The man also runs churches in Port Elizabeth, Cape Town, Johannesburg, Bloemfontein and in the UK.
According to a witness, who did not want to be named, police initially ran through the arrivals doors looking for him.
The source said police found him in the toilets.
The pastor is being represented by Port Elizabeth attorney Alwyn Griebenow, who was also at the airport.
The pastor later arrived at the Directorate for Priority Crime Investigation (the Hawks) offices flanked by police officials.
Lieutenant-Colonel Robert Netshiunda, Hawks spokesperson, said police looked for the pastor at the airport after their hunt did not go as planned.
It is understood the pastor was meant to hand himself over to the Hawks.
“We got information that his flight was delayed, but we could not believe that at face value.
“We went to the airport ourselves, only to find out the flight was on schedule,” said Netshiunda.
Netshiunda said the pastor was charged with human trafficking and additional charges might be added.
On Thursday night, the Port Elizabeth High Court made an order that the pastor’s lawyers be granted access to consult with him.
Griebenow made the urgent application after he claimed that he was denied access to meet his client after his arrest.
The pastor was being held at Mount Road police station and is expected to appear in the Port Elizabeth Magistrate’s Court on Friday.
Social Development MEC Weziwe Thusi welcomed the arrest, commending the police for their swift action and praising the suspect’s victims for coming forward.
The man is accused of luring young women and girls from three provinces to his rented home in uMhlanga and forcing them to have sex with him.
His arrest comes just days after an exposé on the SABC programme Special Assignment.
Thusi said it must have been difficult for the victims to speak out against a man they considered a leader.
“By speaking out, they have reclaimed their power. Hopefully, they can begin to heal now that the wheels of justice are turning in their favour. I hope their courage will inspire other victims to come forward,” she said.
Thusi was “shocked” that a man of the cloth stood accused of such crimes, “but it proves what we have been saying all along that sex pests, child abusers and rapists look like us and live among us”.
It was disturbing that the alleged sex pest used the church as his hunting ground, she said.