The 'Breaking Bad' star picked up Best Lead Actor in a Play for his role as former President Lyndon B. Johnson in Robert Schenkkan's 'All The Way', beating the likes of Chris O'Dowd in 'Of Mice and Men' to the title.
The multiple Emmy award winner, best known for playing chemistry teacher-turned-drug lord Walter White, scored his first ever theatre prize as 'All The Way' was also crowned Best Play.
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.
She said in her emotional acceptance speech: "I want to thank all the shoulders of the strong and brave and courageous women that I am standing on. And most of all Billie Holiday. You deserve so much more than you were given when you were on this earth."
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'.
She enthused, "I am loving it on Broadway", while the play also won best revival.
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'.
The 'Les Miserables' actor, who was hosting for the first time in nine years, joined the cast of the musical 'After Midnight' for a rendition of 'It Don't Mean a Thing (If it Ain't Got that Swing)'.
Another highlight from the ceremony was Neil Patrick Harris - who scooped the Best Actor in a Musical gong - performing a song from 'Hedwig and the Angry Inch', dressed in a miniskirt and blonde wig.
He got into character by giving an audience member a lap dance and even confiscated Samuel L. Jackson's glasses and licked them.
The full list of 2014 Tony Awards winners:
Best Play: 'All the Way'
Best Revival of a Play: 'A Raisin in the Sun'
Best Revival of a Musical: 'Hedwig and the Angry Inch'
Best Book of a Musical: 'A Gentleman's Guide to Love & Murder'
Best Performance by an Actor in a Leading Role in a Play: Bryan Cranston, 'All the Way'
Best Performance by an Actress in a Leading Role in a Play - Audra McDonald, Lady Day at 'Emerson's Bar & Grill'
Best Performance by an Actor in a Featured Role in a Play: Mark Rylance, 'Twelfth Night'
Best Performance by an Actress in a Featured Role in a Musical: Lena Hall, 'Hedwig and the Angry Inch'
Best Performance by an Actor in a Leading Role in a Musical
Neil Patrick Harris, 'Hedwig and the Angry Inch'
Best Direction of a Musical: Darko Tresnjak, 'A Gentleman's Guide to Love & Murder'
Best Direction of a Play: Kenny Leon, 'A Raisin in the Sun'
Best Score: Jason Robert Brown, 'The Bridges of Madison County'
Best Performance by an Actor in a Featured Role in a Musical: James Monroe Iglehart, 'Aladdin'
Best Performance by an Actress in a Featured Role in a Play: Sophie Okonedo, 'A Raisin in the Sun'