Jan Figel, the EU Special Envoy for the Promotion of Freedom of Religion or Belief outside of the European Union, raised the case of Rev Hassan Abduraheem and Abdulmonem Abdumawla on a visit to Sudan earlier this month.
Despite maintaining their innocence, they were convicted of assisting Christian aid worker Petr Jasek with espionage, among other charges, and were sentenced to twelve years in prison in January.
Mr Jašek was pardoned by President Omar al-Bashir last month but the rest of the group remain in jail.
Christian Solidarity Worldwide - an advocacy group for religious freedom - welcomed Figel's call for the pair's release.
Chief Executive Mervyn Thomas said, "We welcome and echo Mr Figel's call for a presidential pardon for Reverend Abduraheem and Mr Abdumawla. Their continued imprisonment after Mr Jašek, the main defendant in their case, was pardoned and released amounts to an injustice."
At a meeting with Sudanese legislators, Figel also raised the issue of church demolitions.
At least 25 churches are scheduled for demolition with authorities saying that the premises are illegal and "trespassing into residential areas".
In 2014, the country banned the construction of new Christian places of worship claiming the nation had enough.
Mervyn Thomas said: "As the EU increases its engagement with Sudan through initiatives such as the Khartoum Process, we urge the EU to ensure that human rights, including freedom of religion or belief, are prioritised in all areas of cooperation."
Sudan is number five on Open Doors' World Watch List for persecution.