Pastor Michael Yat (49) and Pastor Peter Yen Reith (36) had been banned from leaving the country despite their release after they were imprisoned in the capital Khartoum.
The ban was revoked on Thursday but according to charity Middle East Concern (MEC), the National Intelligence and Security Service appealed the decision delaying their escape.
However it's reported that as the process dragged on, the pastors sought other ways of leaving the country. MEC says they succeeded in departing Sudan yesterday, travelling first to their home country and then onwards from there.
The charity's calling on Christians to pray for the pastors that they and their families "know the Lord's clear guidance and provision. That there will be no repercussions for others arising out of the pastors' departure from Sudan. For the lawyer, who is facing charges in a related case. That church leaders in Sudan will know the Lord's wisdom in the face of increasing pressures against them. That all officials involved will love mercy, act justly, learn about Jesus and choose to follow Him."
The pastors,from the Presbyterian Evangelical Church, had been accused of undermining the constitutional system of the Sudanese Penal Code; waging war against the state; disclosure and receipt of official information or documents; arousing feelings of discontent among regular forces; breach of public peace; and offences relating to insulting religious beliefs.
Miles Windsor from Middle East Concern told Premier's News Hour the case isn't over yet.
He warned of the potential for repercussions: "It's certainly not an ideal situation. It does have repercussions potentially for others inside the country."
He said that Sudan did not like to be embarrassed and was likely to punish others for the men escaping.
"There flight could have repercussions for him [their lawyer]. It's not a pleasant situation for Christians in Sudan, they do feel under huge amounts of pressure," he added.
Miles Windsor speaking to Premier's Marcus Jones on the News Hour: