The painting was taken along to a roadshow in Newstead Abbey, near Nottingham, last year by priest Father Jamie MacLeod who now plans to sell it to buy new church bells.
It was identified after the show's host, Fiona Bruce, who was making a show about the artist with expert Philip Mould, saw the painting and thought it might be genuine.
Mr Mould agreed to take a look at it and after a lengthy restoration process the painting was verified by Dr Christopher Brown who is one of the world authorities on van Dyck.
The portrait, originally bought for £400 in a Cheshire antiques shop, is the most valuable painting to ever be identified in the show's 36-year history.
Father Jamie, who runs a retreat house in the Peak District, said, "It's been an emotional experience and it's such great news. It's wonderful that new church bells hopefully will be pealing out to commemorate the centenary of the First World War in 2018."
Anthony van Dyck was the leading court painter in England under King Charles I and is regarded as one of the masters of 17th century art.
A self-portrait recently sold for £12.5 million sparking a fundraising campaign to try to save the painting for the nation.
The work discovered on the show is a portrait of a Magistrate of Brussels which is believed to have been painted as part of the artist's preparation for a 1634 work showing seven magistrates which was eventually destroyed in a French attack on Brussels in 1695.
Fiona Bruce said: "It's everyone's dream to spot a hidden masterpiece, I'm thrilled that my hunch paid off, to discover a genuine van Dyck is incredibly exciting. I'm so pleased for Father Jamie."
"Discoveries of this type are exceptionally rare", said Mr Mould. "The painting's emergence from beneath layers of paint was dramatic. It's been revealed as a thrilling example of van Dyck's skills of direct observation that made him so great a portrait painter."
The discovery will be shown on tonight's episode of Antiques Roadshow at 7pm on BBC One.
Speaking to the BBC Breakfast programme on Sunday morning, Father MacLeod - who made sure to get Bruce's autograph - told how he bought the picture ten years ago.
He said: "I bought it because it was a case of buying a portrait or buying a bookcase, and I decided that I wanted both but that would be greedy. And so the portrait caught my eye.
"There was something about the portrait, something about him - the character, who in once sense looked rather an angry person but the more I looked at him and the years that went on the more I wanted to know more.
"Of course the truth of the matter is that we knew nothing about it."
Father MacLeod said selling the portrait was "a very difficult decision" but that it would help him in his ambition to install new church bells in 2018 to mark the anniversary of the end of First World War.
He said: "When we had lost all our soldiers through the war, nothing really happened regarding having bells hung or recast to commemorate those who had lost their lives. When we had the Second World War, this happened automatically up and down the country.
"I hope that this would be something that will happen all over the country, so that town halls and cities and villages and everywhere else will have church bells rung that will tell out the time but also be that reminder."