It was the second consecutive win for 'Breaking Bag', which re-wrote television history with its story of a chemistry teacher-turned-drug kingpin. The show ended last year after five seasons.
"Thank you so much for this farewell to our show. You have been very kind to us indeed," said show's creator Vince Gilligan, noting that TV was going through its best phase.
The other big winners of the night were comedy series 'Modern Family' and detective drama 'Sherlock: His Last Vow'. Benedict Cumberbatch and Martin Freeman won best actor and best supporting actor in a mini-series while Steven Moffat won best writing in a mini-series for the final episode of 'Sherlock's third series.
Breaking Bad's Cranston picked up his fourth lead-actor Emmy for his performance as Walter White while Aaron Paul won his third supporting-actor award for playing Cranston's sidekick Jesse Pinkman.
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"I don't know why I've been blessed. I love to act and I will do it to my last breath. I'd like to dedicate this word to all the Sneaky Petes (his family nickname) of the world who thought that settling for mediocrity was a good idea because it was safe. Don't do it - take a chance, find a passion, fall in love," Cranston said.
Their co-star Anna Gunn became a two-time winner, and the show was also honoured in the writing category with the award going to Moira Walley-Beckett.