Ruach City Church in Norbury, Croydon, had appealed for as many people as possible to come to the building as they attempted to take back control on Tuesday night.
The travellers had entered the grounds, blocking the congregation from getting inside, in the middle of Monday night.
Trespassers cut the church's locks off and replaced them with their own locks. The church told Premier the police would not let them cut off the group's padlock because it would be criminal damage.
On Tuesday night a large group of the congregation attended a prayer vigil and were able to gain access. The travellers then packed up and left.
"We have the victory," said Bishop John Francis. "We are now in our building. They have gone. We have advanced the Kingdom and the travellers have now left."
It was not the first time travellers had taken over the church. Last time they refused to leave for three months and caused up to £200,000 worth of damage.
Yesterday co-pastor Penny Francis told Premier the group were being rude and appeared drunk.
She said she had witnessed "one of them set fire to rubbish on the ground and say this is what we're going to do to your property".
Ruach City Church thanked the media for their coverage of the situation.
