The critically acclaimed drama, which came to an end last year, celebrated its swansong with a slew of awards including the night's top prize, Outstanding Drama, and Outstanding Actor in a Drama for Bryan Cranston.
Aaron Paul and Anna Gunn also earned Outstanding Supporting Actor and Best Supporting Actress in a Drama, respectively, for the show.
Breaking Bad creator Vince Gilligan said: "Thank you so much for this wonderful farewell, you have been very kind to us indeed."
Modern Family was crowned Outstanding Comedy Series for a fifth consecutive year and actor Ty Burrell was lauded for his portrayal of Phil Dunphy with the Outstanding Supporting Actor in a Comedy award.
Veep star Julia Louis-Dreyfus and The Big Bang Theory funnyman Jim Parsons continued to rein over the comedy acting categories, winning Outstanding Actress and Outstanding Actor in a Comedy yet again. The award marks Julia's third consecutive nod for her hit HBO show, while Jim is now a four-time Emmy winner for his role as socially-challenged scientist Sheldon Cooper.
The humble comedian put his big win down to luck, telling the audience: "There is no accounting for taste and it's with good fortune that I stand up here tonight."
The Good Wife actress Julianna Margulies topped the Outstanding Actress in a Drama category and paid tribute to her fellow nominees, enthusing: "What a wonderful time for women on television."
Sherlock star Benedict Cumberbatch waved the flag for the Brits by winning Outstanding Actor in a Miniseries or Movie, beating his co-star Martin Freeman—who was nominated for his role in Fargo—and Oscar nominee Chiwetel Ejiofor. But Martin didn't go home empty-handed as he earned Outstanding Supporting Actor in a Miniseries or Movie for his role as Dr. John Watson in Sherlock.
Jessica Lange, who recently announced she will retire from acting soon, was honored with another Emmy Award for Outstanding Actress in a Miniseries or Movie for American Horror Story: Coven.
This year's Emmy Awards weren't without controversy, however, as social media users blasted a "sexist" skit which saw Modern Family beauty Sofia Vergara pose on a rotating platform while the Academy of Television Arts & Sciences president Bruce Rosenblum gave his annual speech.
One angry viewer wrote on Twitter: "aaaand with that sexist Sophia Vergara bit, my TV is now off. Didn't last long. (sic)"
Another sarcastically wrote: "Sophia Vergara was literally just used as a prop, because women are props. Cool #Emmys (sic)"
2014 Primetime Emmy Awards winners:
Outstanding Drama: Breaking Bad
Outstanding Comedy: Modern Family
Outstanding Actor in a Drama Series: Bryan Cranston, Breaking Bad
Outstanding Actress in a Drama Series: Julianna Margulies, The Good Wife
Outstanding Supporting Actor in a Drama Series: Aaron Paul, Breaking Bad
Outstanding Supporting Actress in a Drama Series: Anna Gunn, Breaking Bad
Outstanding Actor in a Comedy Series: Jim Parsons, The Big Bang Theory
Outstanding Actress in a Comedy Series: Julia Louis-Dreyfus, Veep
Outstanding Supporting Actor in a Comedy Series: Ty Burrell, Modern Family
Outstanding Supporting Actress in a Comedy Series: Allison Janney, Mom
Outstanding Miniseries: Fargo
Outstanding TV Movie: The Normal Heart
Outstanding Actor in a Miniseries or Movie: Benedict Cumberbatch, Sherlock
Outstanding Actress in a Miniseries or Movie: Jessica Lange, American Horror Story: Coven
Outstanding Supporting Actor in a Miniseries or Movie: Martin Freeman, Sherlock
Outstanding Supporting Actress in a Miniseries or Movie: Kathy Bates, American Horror Story: Coven
Outstanding Reality Competition Program: The Amazing Race
Outstanding Structured Reality Program: Shark Tank
Outstanding Unstructured Reality Program: Deadliest Catch
Outstanding Variety Series: The Colbert Report
Outstanding Host for a Reality Program: Jane Lynch, Hollywood Game Night