The acclaimed drama from New Zealand director Jane Campion was beaten by Behind the Candelabra for the Best Miniseries or Movie award.
Campion also lost out in the Best Director for a Miniseries or Movie category.
It went to Stephen Soderbergh for Behind the Candelabra.
Laura Linney won the Best Actress in a Miniseries/Movie prize for The Big C despite Top of the Lake star Elisabeth Moss turning in a critically acclaimed performance.
The losses meant Top of the Lake failed to pick up any awards at today's awards ceremony.
Australia's Alan Arkapaw won best cinematography in a miniseries-telemovie for his work on the show in a separate ceremony held last week.
Jeff Daniels, who plays a jaded anchorman in HBO's "The Newsroom," scored an upset win for the best actor in a drama at the Primetime Emmys, while Claire Danes was a return winner as best drama actress for her role as a bipolar CIA agent in "Homeland".
Daniels beat front-runner Bryan Cranston, who was looking for this fourth best actor Emmy in his role as unlikely drug kingpin Walt White in the AMC drama "Breaking Bad," and Kevin Spacey, who made waves as a cutthroat congressman in "House of Cards," from online streaming company Netflix.
"I didn't expect this," Daniels said. "I usually don't win anything. The last thing I won was for 'The Squid and the Whale,' best actor over 50 from the AARP. With all due respect to the AARP, this is better."
Jane Campion and Garth Davis missed out the screenplay award, while Peter Mullan (supporting actor) and Elisabeth Moss (outstanding actress) were also overlooked.
TV's top honours both celebrated and mocked the latest trends of an industry in transition, like binge-watching, mobile viewing and online streaming pioneered in the last year by Netflix.
Making light of the television fads of the day host Neil Patrick Harris opened the televised ceremony enclosed in a room trying to catch up on every episode.
"Right now, I am watching an episode of 'American Horror Story: Asylum' on my contact lens," Harris joked with the audience at the Nokia Theatre in Los Angeles.
The lead comedy acting awards were less of a surprise than the drama category.
Julia Louis-Dreyfus won the best comedy actress Emmy for the second year in a row for her role as hapless U.S. Vice President Selina Meyer on HBO's "Veep."
Jim Parsons picked up his third lead comedy actor win for his role as the nerdy and neurotic Sheldon Cooper on CBS' "The Big Bang Theory."
But the awards kicked off with upsets in the two supporting actor awards in comedy going to first-time Emmy winners.
Merritt Wever, who plays a quirky nurse on Showtime's dark comedy "Nurse Jackie," won best supporting actress in a comedy series and gave a novel acceptance speech. "Thank you so much. I've got to go, bye," Wever said.
Tony Hale took best supporting actor for comedy for his role as a body man for the U.S. vice president in HBO's "Veep."
Actress and comedian Tina Fey and Tracey Wigfield won best writing for a comedy for NBC's "30 Rock," which ended this year.
The best writing award for drama went to the late "Homeland" writer Henry Bromell who died this year. His father was a CIA station chief and Bromell was credited by his fellow "Homeland" writers for bringing CIA bona fides to the story.
Anna Gunn won best supporting actress in a drama for her role as the wife Skyler on "Breaking Bad." Best supporting actor in a drama series went to Bobby Cannavale for his role as a ruthless Prohibition-era gangster in HBO's "Boardwalk Empire."
BINGE-WATCHING 'BREAKING BAD'
The top comedy prize, for best series, will be announced toward the end of the broadcast. The favorite is three-time winner "Modern Family," but "Louie," featuring New York comedian Louis C.K., could surprise. "30 Rock" is competing for its final season, alongside HBO's "Girls" and "Veep" and "The Big Bang Theory" from CBS.
Vying for the most coveted award of the night, best drama series, are "Breaking Bad," the favourite to win, last year's winner "Homeland" from Showtime, HBO's medieval fantasy "Game of Thrones," British period drama "Downton Abbey" (PBS), four-time winner "Mad Men," and political thriller "House of Cards."
If "House of Cards," with nine nominations overall, wins in any of the major categories, it will be the first time a programme made specifically for online streaming wins a major Emmy award.
"We're the new kids on the block and it's exciting, it's progressive, and I'm excited about the future," Spacey said on the red carpet. "I think for audiences it's incredible because they get a chance to decide how they want to view something and we're giving them the control."
"Breaking Bad," a gritty series about a chemistry teacher who cooks crystal meth and transforms into a ruthless drug kingpin, could win the best drama award for the first time.
AMC split the final season of "Breaking Bad" in two, enjoying a surge in ratings and a crescendo of critical and social media buzz perfectly timed to when Emmy voters were casting their ballots.
The first six episodes of the eight-episode ending to Walter White's saga, released weekly starting in August, averaged 5.2 million viewers, more than double last year's audience, according to AMC.
The Emmys are handed out by the Academy of Television Arts and Sciences in a televised ceremony from Los Angeles.
They honour a broad swath of television production, from the pinnacle prize of best drama series to more obscure ones like best sound mixing for non-fiction programming. There are 537 separate nominations and HBO alone picked up 108 of those, more than twice its closest competitors, broadcasters CBS and NBC with 53 each.
A partial winners list from the Emmy Awards in Los Angeles:
Best Drama: Breaking Bad
Best Comedy: Modern Family
Outstanding Miniseries or Movie: Behind The Candelabra
Outstanding Lead Actor in a Miniseries or Movie: Michael Douglas, Behind The Candelabra
Outstanding Supporting Actress in a Miniseries or Movie: Ellen Burstyn, Political Animals
Outstanding Directing for a Miniseries, Movie or Dramatic Special: Steven Soderbergh, Behind The Candelabra
Outstanding Supporting Actor in a Miniseries or Movie: James Cromwell, American Horror Story: Asylum
Outstanding Writing for a Miniseries, Movie or Dramatic Special: Abi Morgan, The Hour
Outstanding Variety Series: The Colbert Report
Outstanding Choreography: Derek Hough, Dancing with the Stars
Outstanding Directing in a Variety Series: Don Roy King, Saturday Night Live
Outstanding Writing in a Variety Series: The Colbert Report
Outstanding Directing in a Drama Series: David Fincher, House of Cards
Outstanding Guest Actor in a Drama Series: Dan Bucatinsky, Scandal
Outstanding Guest Actress in a Drama Series: Carrie Preston, The Good Wife
Outstanding Lead Actress in a Drama Series: Claire Danes, Homeland
Outstanding Supporting Actress in a Drama Series: Anna Gunn, Breaking Bad
Outstanding Writing in a Drama Series: Henry Bromell, Homeland
Outstanding Lead Actress in a Miniseries or Movie: Laura Linney, The Big C
Outstanding Lead Actor in a Comedy Series: Jim Parsons, The Big Bang Theory
Outstanding Directing in a Comedy Series: Gail Mancuso, Modern Family
Outstanding Guest Actor in a Comedy Series: Bob Newhart, The Big Bang Theory
Outstanding Guest Actress in a Comedy Series: Melissa Leo, Louie
Outstanding Lead Actress in a Comedy Series: Julia Louis-Dreyfus, Veep
Outstanding Supporting Actor in a Comedy Series: Tony Hale, Veep
Outstanding Writing in a Comedy Series: Tina Fey & Tracey Wigfield, 30 Rock
Outstanding Supporting Actress in a Comedy Series: Merritt Wever, Nurse Jackie
