The beloved U.S. funnywoman had held on to the prize since 2005, but faltered at the ceremony on Sunday (30Aug09) when she came up against The View's feisty foursome Whoopi Goldberg, Joy Behar, Elisabeth Hasselbeck and Barbara Walters.
But it wasn't all bad for DeGeneres - her daily chatshow pulled back by picking up four awards during the night.
Fellow chatshow hosts Rachael Ray and Tyra Banks also walked away with prizes, winning Best Entertainment and Best Informative programme for the respective TV shows.
U.S. soap opera The Bold And The Beautiful took Best Drama, while Best Actor went to The Young And The Restless' Christian LeBlanc and Susan Haskell, from One Life To Live, was named Best Actress.
Haskell was also celebrating after her show scooped the most awards of the night, tied with All My Children - winning five Emmys in total.
PBS' Sesame Street received the lifetime achievement award in recognition of its 40-year run.
The ceremony was hosted by Ugly Betty star Vanessa Williams at the Orpheum Theater in Los Angeles.