The work was bought 12 years ago by Father Jamie MacLeod from an antiques shop in Cheshire and was identified after the show's host, Fiona Bruce, thought it might be genuine.
Mrs Bruce, who was making a show about the artist with expert Philip Mould, asked him to look at it and after restoration the painting was verified by Dr Christopher Brown, a leading authority on Van Dyck.
Fr MacLeod, who runs a retreat in the Peak District, said: "It has been a blessing to own this magnificent portrait which has given me great pleasure over the years.
"I will be sad to part with it, though the proceeds will be put to excellent use, going towards the acquisition of new church bells for Whaley Hall Ecumenical Retreat House in Derbyshire to commemorate the centenary of the end of the First World War in 2018."
Fr MacLeod has previously outlined his plans to restore the former Clydebank Memorial Church's Emmanuel bell, which was rung to warn people living by the Clyde of an impending attack during the Blitz.
The painting, believed to be a sketch for a work called the Magistrates Of Brussels, will be sold by auction at Christie's London sale of Old Master and British Paintings in June.