"Veep" was named best comedy series and its star, Julia Louis-Dreyfus, won a record-breaking fifth Emmy as best comedy actress.
"The People v OJ Simpson", which is the dramatic retelling of the infamous O J Simpson's murder trial, was honoured for its writing and captured several acting awards.
Courtney B Vance bagged best actor in limited series or movie, Sarah Paulson won best actress and the best supporting actor honour to Sterling K Brown.
HBO series "Game of Thrones", the fantasy saga based on George RR Martin's novels, made Emmy history, pushing its lifetime total number of awards to 38 - one more than "Frasier", the previous all-time record holder.
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Besides best drama, "GOT" won David Benioff and DB Weiss the best writing in a drama series honour and best directing in a drama series for Miguel Sapochnik.
The series already became the most-honoured drama series after picking up nine Emmys at the Creative Arts ceremony last weekend. Overall it won 12 Emmys this year, out of 23 total nominations.
"Oh, my God. Please tell me you're seeing this too," Malek, who plays an emotionally troubled engineer caught up in a dangerous hacking conspiracy, said after winning the honour.
The Emmys also did not shy from honouring minority talents as Indian-origin actor-writer-director Aziz Ansari and Alan Yang received the best writing for a comedy series honour for "Master of None."
Louis-Dreyfus used her victory at the Jimmy Kimmel-hosted ceremony, which was witnessed several starts making sharp political jabs, to take a dig at GOP contender Donald Trump.
A shaking Louis-Dreyfus ended her speech by dedicating
the trophy to her father, who she said died on Friday.
Jeffrey Tambor captured his second consecutive best comedy actor trophy for "Transparent," in which he plays a transgender character.
He called for Hollywood to make him the last non-transgender actor to get such a role.
Maggie Smith was named best supporting actress in a drama series for the final season of "Downton Abbey." It was her third win for playing the role of a dowager and like always she didn't attend the ceremony.
"Saturday Night Live" cast member Kate McKinnon won the trophy for best supporting actress in a comedy for, officially, playing various characters.
"Thank you, Ellen DeGeneres, thank you, Hillary Clinton," she said, naming two of the famous people she's caricatured on the show.
Ben Mendelsohn of "Bloodline" won best supporting drama actor. John Oliver received the best variety talk series award for "Last Week Tonight with John Oliver."
Louie Anderson was honoured as best supporting actor in a comedy series for his portrayal of a loving but tough mom in "Baskets."
The award for best direction for a limited series, movie or drama went to Susanne Bier for "The Night Manager." "The Voice" was named best reality-competition program.
The best television movie honour was given to "Sherlock: The Abominable Bride.