The soap opera that began in 1965 beat out defending champion "General Hospital" and former three-time winner "The Bold and the Beautiful," among others.
The category included the only four remaining soaps still airing on the broadcast networks in addition to "One Life to Live," which has found new life on the Internet after being canceled.
Doug Davidson of "The Young and the Restless" and Heather Tom of "The Bold and the Beautiful" won lead acting honors.
There was unexpected glitch when the ladies of "The Talk" presented outstanding talk show informative. Aisha Tyler opened the envelope and quickly realized it was the wrong one.
"The Dr. Oz Show" was then announced as the winner.
"I was having heart palpitations, real ones," Dr. Mehmet Oz said onstage.
Corbin Bernsen uttered two expletives during the in memoriam tribute that included his late mother Jeanne Cooper of "The Young and the Restless."
In an upset, first-time nominee "CBS Sunday Morning" beat out heavyweights "Good Morning America" and the "Today Show" for outstanding morning program.
"We snuck in while nobody was looking," host Charles Osgood said.
Ricki Lake, whose daytime comeback has been canceled, won outstanding talk show host.
Ben Bailey of "Cash Cab" picked up his third win as outstanding game show host, beating out five-time winner Alex Trebek of "Jeopardy!" among others.
The ceremony pitted the only four remaining soaps still airing on the broadcast networks against one that found new life on the Internet.
"The Ellen DeGeneres Show" earned its seventh trophy as outstanding talk show entertainment.
"Good Morning America" weather anchor Sam Champion, along with HLN network's A.J. Hammer and Robin Meade, hosted the show on HLN.
The 40th anniversary of the Daytime Emmys was recognized with a past, present and future theme woven throughout the show.
The Daytime Emmys moved back to Southern California last year after being in Las Vegas for two years, and its ratings, like many of the daytime shows it celebrates, have bounced up and down in recent years. Last year, HLN scored its highest numbers ever for a scheduled non-news broadcast when it aired the awards for the first time.
Kevin Clash, who played the Elmo character on "Sesame Street" before resigning last November, won three trophies, including outstanding performer in a children's series.
Ziggy Marley won for outstanding original song, writing the music and lyrics for "I Love You Too" for the Disney Channel show "3rd & Bird!"
Syndicated shows were second with nine creative arts trophies, followed by HUB Network and Nickelodeon with seven each. ABC received four awards, while Disney Channel and NBC had three each. In a sign of changing times, Facebook and YouTube each received a trophy.
The Associated Press contributed to this report.