Bowen, who plays Claire Dunphy in the hit U.S. TV show, beat out veteran stars Jane Lynch (Glee) and Betty White (Hot In Cleveland), her Modern Family co-star Sofia Vergara, 30 Rock's Jane Krakowski, and Saturday Night Live's Kristen Wiig for Outstanding Supporting Actress in a Comedy Series.
Accepting the award, a stunned Bowen gasped, "Oh my god, are you kidding me! I don't know what to talk about in therapy next week now! I won something!"
She then thanked the show's writers and Emmy voters, and paid tribute to her "two husbands", saying, "For now I just want to thank the two most important people in my life, my two husbands: my TV husband Ty Burrell, who helps to manage my fear on a daily basis and who makes Claire Dunphy possible; and my real husband, Scott, happy anniversary."
Bowen's win occurred just days after she celebrated her seventh wedding anniversary to real estate investor Scott Phillips on 9 September.
And it was a double joy for the Modern Family team when Burrell claimed the second award of the night, for Outstanding Supporting Actor in the same genre.
He remembered his late father as he collected the award, triumphing over onscreen pals Ed O'Neill, Jesse Tyler Ferguson and Eric Stonestreet for the prize, in addition to Glee's Chris Colfer and Jon Cryer from Two and a Half Men.
The 63rd Primetime Emmy Awards are being presented by Jane Lynch at Los Angeles' Nokia Theatre.