The 58-year-old multiple Emmy award winner, best known for playing chemistry teacher-turned-drug lord Walter White in 'Breaking Bad', scored his first ever theatre prize as 'All The Way' was also crowned best play, reported USA Today.
He beat the likes of Chris O'Dowd in 'Of Mice and Men' to the title.
Audra McDonald made history by winning her sixth Tony for her performance as Billie Holiday in 'Lady Day at Emerson's Bar & Grill', becoming the only woman to win a Tony in all four acting categories.
He got into character by giving an audience member a lap dance and even confiscated Samuel L Jackson's glasses and licked them. 'Hedwig and the Angry Inch' was named best revival of a musical.
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Meanwhile, British actress Sophie Okonedo was given the featured actress in a play prize for her Broadway debut as Denzel Washington's wife in 'A Raisin in the Sun'.
The ceremony was hosted by Hugh Jackman at Radio City Music and boasted performances by Tony nominated singer Idina Menzel, Gladys Knight and the cast of 'Cabaret'.