The hit fantasy series - which is partly filmed in Northern Ireland - topped the 2014 nominations list with 19 nods in total for its cast and crew.
But during the ceremony on Monday the programme was overlooked for the major awards of the night, including best drama, best supporting actor for Peter Dinklage and best supporting actress for Lena Headey.
The show did win a number of technical awards, including best art direction, best special and visual effects and best costume.
The big winner of the night was the hit series Breaking Bad which was named best drama series.
The stars of the drug drama about a chemistry teacher-turned-meth dealer also celebrated big wins in the acting categories.
Bryan Cranston was named best actor, while Aaron Paul and Anna Gunn were awarded the best supporting actor and actress gongs respectively.
Collecting his award, Cranston said: "I have gratitude for everything that has happened."
The show's creator, Vince Gilligan, said: "Thank you for this wonderful farewell to our show."
The BBC series Sherlock scooped a hat-trick of awards, with its stars Benedict Cumberbatch and Martin Freeman winning awards for actor and supporting actor in a mini-series or movie for their parts as Sherlock Holmes and Dr Watson.
The detective drama's writer, Steven Moffat, picked up the award for writing in a mini-series, movie or dramatic special.
Reflecting on his Emmy success, which he said he hoped would get more people watching the show, he said: "I didn't think to prepare a single word because I didn't think we could win."
Other winners included Fargo, which was screened on Channel 4 earlier this year and starred Freeman as the lead character.
It won the Emmy for a mini-series.
It was a less successful night for period drama Downton Abbey, which had a handful of nominations but neither Michelle Dockery, who plays Lady Mary Crawley, nor her co-stars Dame Maggie Smith, Joanne Froggatt or Jim Carter managed to win.
Ricky Gervais's Derek missed out to Big Bang Theory's Jim Parsons in the best actor in a comedy series category.
Meanwhile, Billy Crystal paid tribute to Robin Williams, calling him "the greatest friend you could ever imagine".
Crystal, who had an image of the Good Morning Vietnam actor above him, said: "He made us laugh, big time."
The City Slickers actor added: ''It's very hard to talk about him in the past because he was so present in all of our lives. He was the brightest star in the comedy galaxy.''
Crystal reflected on the Mrs Doubtfire star's legacy and how he will be remembered years from now.
''And you'll think to yourself 'Robin Williams, what a concept','' he said.
2014 Emmy Awards winners:
Outstanding Drama Series - Breaking Bad
Outstanding Lead Actress in a Drama Series - Julianna Margulies, The Good Wife
Outstanding Lead Actor in a Drama Series - Bryan Cranston, Breaking Bad
Outstanding Supporting Actress in a Drama Series - Anna Gunn, Breaking Bad
Outstanding Supporting Actor in a Drama Series - Aaron Paul, Breaking Bad
Outstanding Writing for a Drama Series - Breaking Bad
Outstanding Directing for a Drama Series - True Detective
Outstanding Comedy Series - Modern Family
Outstanding Lead Actress in a Comedy Series - Julia Louis-Dreyfus, Veep
Outstanding Lead Actor in a Comedy Series - Jim Parsons, The Big Bang Theory
Outstanding Supporting Actress in a Comedy Series - Allison Janney, Mom
Outstanding Supporting Actor in a Comedy Series - Ty Burrell, Modern Family
Outstanding Writing for a Comedy Series - Louie
Outstanding Directing for a Comedy Series - Modern Family
Outstanding Miniseries - Fargo
Outstanding Television Movie - The Normal Heart
Outstanding Lead Actress in a Miniseries or a Movie - Jessica Lange, American Horror Story: Coven
Outstanding Lead Actor in a Miniseries or a Movie - Benedict Cumberbatch, Sherlock: His Last Vow
Outstanding Supporting Actress in a Miniseries or a Movie - Kathy Bates, American Horror Story: Coven
Outstanding Supporting Actor in a Miniseries or a Movie - Martin Freeman, Sherlock: His Last Vow