Aniston was named favorite female star, while Vaughn was picked by the public as favorite leading man.
"You all have supported me since the days of Friends," Aniston told the audience, "just through all of it – good work, bad work and the ugly. I just thank you." Playing on the movie's title and her real life, she added: "Thank you for loving The Break-Up – I did."
Aniston also poked a little fun at Britney Spears, quipping about the short skirt she was wearing: "Man, I tell you, it's a lucky thing we do wear underwear, huh?"
Later in the show, by which time his costar and ex-girlfriend had left, Vaughn thanked Aniston in his acceptance speech and called her "one of the great people in Hollywood."
"I've said this before, but the fact that this award comes from the people makes it that much more special," he said. "Thanks for the honor. Thanks for keeping me employed. You're the boss."
Grey's Anatomy was a double winner: favorite TV drama and Patrick Dempsey, favorite male TV star.
"Thank you for a second chance!" Dempsey told the crowd. "I'm very fortunate to be part of a great ensemble." To the show's creator, Shonda Rhimes, he said: "Thank you for creating Dr. McDreamy, it's changed my life."
And Desperate Housewives's Eva Longoria, who was named favorite female TV star, told the crowd: "If it wasn't for the people, I'd never win an award."
Justin Timberlake's "SexyBack" was named favorite R&B song, while Carrie Underwood and Kenny Chesney were cited as favorite singers.
The ceremony, broadcast from the Los Angeles Shrine Auditorium, aired on CBS and was hosted by Queen Latifah.