The two panels, depicting St Victor of Marseilles and St Margaret of Antioch, were stolen from Holy Trinity Church in Torbryan, Newton Abbot, in August 2013.
They were found by the Metropolitan Police during a raid in south London after being spotted by a private collector in an online sale.
An appeal to repair the damage caused to the panels during the theft has been launched by the Churches Conservation Trust.
Chief executive Crispin Truman said: "The Churches Conservation Trust cares for 347 churches around the country, and the Torbryan rood screen is one of the highlights of this internationally significant collection.
"The theft of these unique artworks from Holy Trinity was a real blow, so we're delighted that they are now back in our hands.
"Unfortunately the damage caused as the thieves hacked them out of the church will cost a lot to put right, so today we have launched a campaign to raise the £7,000 needed to conserve them and repair the damage.
"The Churches Conservation Trust is committed to displaying unique artefacts like these panels in their original setting and open to the public for everyone to see and enjoy.
"We now need to raise the funds to return these panels to their beautiful medieval church, in a tranquil wooded Devon valley that has remained unchanged for centuries."
