The best comedy award went to "Modern Family," the fourth year in a row it has topped the category, while "Big Bang Theory" star Jim Parsons took the best comedy actor prize for a third time at the Emmys, television's version of the Oscars.
Liberace biopic "Behind the Candelabra" was the other big winner of the night, taking home prizes for best miniseries/TV movie, best actor for Michael Douglas as the flamboyant gay piano icon and best director Steven Soderbergh.
The critically-acclaimed "Breaking Bad," about a chemistry teacher turned drug lord Walter White, won the top drama prize only a weekend before its series finale next week after five seasons.
Show producer and writer Vince Gilligan looked shocked as he took the stage at the climax of the 65th Primetime Emmy awards show in Los Angeles. His show had been nominated for the top prize three times before.
"I thought this was going to be 'House of Cards'," he said, before adding that it could have been one of the other four shows nominated: "Downton Abbey," "Game of Thrones," "Homeland" or "Mad Men."
Perhaps the biggest upset of the night was for Jeff Daniels, who won best drama actor Emmy for his role as TV news anchor Will McAvoy in HBO's "The Newsroom."
The frontrunners had been "Breaking Bad" star Bryan Cranston, who has already won it three times, and "House of Cards" star Kevin Spacey for his turn as scheming congressman Francis Underwood.
Claire Danes won best drama actress for the second year in a row for her turn as bipolar CIA agent Carrie Mathison in "Homeland," besting rivals including "House of Cards" co-star Robin Wright, who plays Spacey's character's wife Claire.
Disappointed fans of Kerry Washington had hoped she would become the first African American to win best actress in a drama for her role in ABC's political thriller "Scandal." She was the first nominated in the category since 1995.
On the comedy front, the top prize went to "Modern Family," about the dysfunctional antics of Jay Pritchett and his extended family in Los Angeles.
Political comedy "Veep" scored two wins with best actress for Julia Louis-Dreyfus and best supporting actor for Tony Hale.
Elton John meanwhile made a moving tribute to Liberace, playing a new song and acknowledging the gay piano icon's influence on his own music "and my dress sense," saying: "This guy played a mean piano."
Douglas, accepting the Emmy for his turn as Liberace, got laughs when paying tribute to co-star Matt Damon, who plays Liberace's gay lover Scott Thorson.
"This is a two-hander," he said, to widespread titters. "And Matt, you're only as good as your other hand ... The only reason I'm standing here is because of you."
Gripping the Emmy statuette, he said he would have to share it with Damon, who was also nominated in the same category. "You want the bottom or the top?" Douglas asked Damon, bringing the house down.
But the biggest loser of the night was "House of Cards," which had hoped to symbolize the direction the TV industry is going -- online.
The Netflix political drama aimed to become the first online-only series to win in major categories, but only took home a prize for best directing for David Fincher.
The series' success highlights the changes underway in the industry, with more and more viewers "cutting the cable" and watching favorite shows via the Internet on cellphones, tablets and so-called "smart TVs."
FULL LIST OF WINNERS
— Drama Series: “Breaking Bad,” AMC.
— Actor, Drama Series: Jeff Daniels, “The Newsroom,” HBO.
— Actress, Drama Series: Claire Danes, “Homeland,” Showtime.
— Supporting Actor, Drama Series: Bobby Cannavale, “Boardwalk Empire,” HBO.
— Supporting Actress, Drama Series: Anna Gunn, “Breaking Bad,” AMC.
— Directing, Drama Series: David Fincher, “House of Cards,” Netflix.
— Writing, Drama Series: Henry Bromell, “Homeland,” Showtime.
— Comedy Series: “Modern Family,” ABC.
— Actor, Comedy Series: Jim Parsons, “The Big Bang Theory,” CBS.
— Actress, Comedy Series: Julia Louis-Dreyfus, “Veep,” HBO.
— Supporting Actor, Comedy Series: Tony Hale, “Veep,” HBO.
— Supporting Actress, Comedy Series: Merritt Wever, “Nurse Jackie,” Showtime.
— Directing, Comedy Series: Gail Mancuso, “Modern Family,” ABC.
— Writing, Comedy Series: Tina Fey, Tracey Wigfield, “30 Rock,” NBC.
— Miniseries or Movie: “Behind the Candelabra,” HBO.
— Actor, Miniseries or Movie: Michael Douglas, “Behind the Candelabra,” HBO.
— Actress, Miniseries or Movie: Laura Linney, “The Big C: Hereafter,” Showtime.
— Supporting Actor, Miniseries or Movie: James Cromwell, “American Horror Story: Asylum,” FX Networks.
— Supporting Actress, Miniseries or Movie: Ellen Burstyn, “Political Animals,” USA.
— Directing, Miniseries or Movie: Steven Soderbergh, “Behind the Candelabra,” HBO.
— Writing, Miniseries or Movie: Abi Morgan, “The Hour,” BBC America.
— Reality-Competition Program: “The Voice,” NBC.
— Variety Series: “The Colbert Report,” Comedy Central.
— Writing, Variety Series: “The Colbert Report,” Comedy Central.
— Directing, Variety Series: Don Roy King, “Saturday Night Live,” NBC.
— Choreography: Derek Hough, “Dancing With the Stars,” ABC.
