The 59-year-old was awarded the best actor gong at the Royal Festival Hall in London last on Sunday night.
The six-part BBC One programme, which aired last year, tells the story of Fr Kerrigan - a well-respected Catholic priest presiding over a large parish on the outskirts of a major city in northern England.
Picking up the award, the actor from Sheffield said: "Thank you very much everyone, and thank you Bafta. This means a great deal to me and I am really honoured.
"I do not think I would be in this situation without the great mind and great writing of Jimmy McGovern, who is an inspiration to me. He is an incredible man who shines a light on some of the darker aspects of our society."
Anna Friel also won best supporting actress for her role in the drama.
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