The US sitcom took home the top Comedy Series prize as well as gongs for Supporting Actress and Supporting Actor in a Comedy for Julie Bowen and Eric Stonestreet, while the ABC show's helmer Steven Levitan won the Director award.
Psychological thriller 'Homeland' upstaged some of the more established programmes by winning four drama series honours including the main prize for the category and Series Actor and Actress in a Drama prizes for Damian Lewis and Claire Danes respectively.
Damian introduced himself to the audience as "one of those pesky Brits" and later admitted he thought 'Breaking Bad' star Bryan Cranston, who has won the accolade three times, would be victorious in the category again this year.
Speaking to CNN backstage, he said: "I was quite convinced that he'd be walking up again tonight."
Dame Maggie Smith took home the Supporting Actress prize for her role in British drama 'Downton Abbey' and Jimmy Fallon won the Guest Actor in a Comedy prize for his cameo on 'Saturday Night Live'.
'Two and a Half Men' picked up two prizes thanks to Jon Cryer and Kathy Bates winning the Lead Actor and Guest Actress in a Comedy accolades.
Kevin Costner won the Best Actor prize for starring in a Miniseries or Movie for his part in Civil War drama miniseries 'Hatfields and McCoys' and Julianne Moore won the respective Best Actress accolade for 'Game Change'.
The ceremony - which was hosted by Jimmy Kimmel at the Nokia Theatre in Los Angeles - ended with a touching moment as Michael J. Fox, who has been battling Parkinson's disease for several years, receiving a standing ovation when he went up to present the final award of the night.
He said: "I'm steady as a rock."
Selected list of winners at the 64th annual Primetime Emmy Awards:
Drama Series: 'Homeland,' Showtime.
Actress, Drama Series: Claire Danes, 'Homeland,' Showtime.
Actor, Drama Series: Damian Lewis, 'Homeland,' Showtime.
Supporting Actor, Drama Series: Aaron Paul, 'Breaking Bad,' AMC.
Supporting Actress, Drama Series: Maggie Smith, 'Downton Abbey,' PBS.
Writing, Drama Series: Alex Gansa, Howard Gordon, Gideon Raff, 'Homeland,' Showtime.
Directing, Drama Series: Tim Van Patten, 'Boardwalk Empire,' HBO.
Comedy Series: 'Modern Family,' ABC.
Actor, Comedy Series: Jon Cryer, 'Two and a Half Men,' CBS.
Actress, Comedy Series: Julia Louis-Dreyfus, 'Veep,' HBO.
Supporting Actress, Comedy Series: Julie Bowen, 'Modern Family,' ABC.
Supporting Actor, Comedy Series: Eric Stonestreet, 'Modern Family,' ABC.
Writing, Comedy Series: Louis C.K, 'Louie,' FX Networks.
Directing, Comedy Series: Steven Levitan, 'Modern Family,' ABC.
Miniseries or Movie: 'Game Change,' HBO.
Actress, Miniseries or Movie: Julianne Moore, 'Game Change,' HBO.
Actor, Miniseries or Movie: Kevin Costner, 'Hatfields & McCoys,' History.
Supporting Actress, Miniseries or Movie: Jessica Lange, 'American Horror Story,' FX Networks.
Supporting Actor, Miniseries or Movie: Tom Berenger, 'Hatfields & McCoys,' History.
Directing, Miniseries, Movie or Dramatic Special: Jay Roach, 'Game Change,' HBO.
Writing, Miniseries, Movie or Dramatic Special: Danny Strong, 'Game Change,' HBO.
Reality-Competition Program: 'The Amazing Race,' CBS.
Host, Reality-Competition Program: Tom Bergeron, 'Dancing With the Stars,' ABC.
Variety, Music or Comedy Series: 'The Daily Show With Jon Stewart,' Comedy Central.
Writing for a Variety Special: Louis C.K., 'Louis C.K. Live at the Beacon Theatre,' FX Networks.
Directing, Variety, Music or Comedy Special: Glenn Weiss, 65th Annual Tony Awards, CBS.