On her Facebook profile, the 17-year-old daughter of the Republican presidential hopeful listed herself as a member of Obama's Facebook group, "Barack Obama (One Million Strong for Barack)."
She left the group Monday morning after the online magazine Slate sent an inquiry and later in the day, a spokeswoman said she did not intend to comment on the 2008 race.
The New York Times reported that Obama was asked about Caroline's support during a campaign swing in Iowa.
"That's very nice," the Democratic presidential candidate said. "We think it's wonderful that we are attracting support from young people all across the country. I can't wait to meet her."
Giuliani, who was also campaigning in Iowa, declined to comment on his daughter's political preference.
"My daughter I love very much," he told reporters outside an Italian restaurant in Clear Lake. "I have great respect for her, and I'm really proud of her, and I don't comment on children, because I want to give them the maximum degree of privacy.
"The best thing to do, if you want to ask the press to leave the children alone, the best way to do it is not to comment on them one way or the other, except to say you're very proud of them, and you love them very much, which I do," he said.
Caroline Giuliani's spokeswoman offered this explanation: "Before the presidential campaign got under way, Caroline added herself to a list on Facebook as an expression of interest in certain principles. "It was not intended as an indication of support in a presidential campaign, and she has removed it."
Her profile can be viewed by Facebook users who have access to New York City's Trinity School or Harvard University networks. Caroline, who is Giuliani's daughter with his second wife, Donna Hanover, recently graduated from Trinity and will attend Harvard in the fall.
Slate magazine posted a screen shot of her profile, which uses a slightly different last name. She lists herself as having liberal political views.
Giuliani, a leading Republican candidate, has asked for privacy to deal with strained relationships in his family. Son Andrew, 21, has said their relationship became distant after Giuliani's messy divorce from the children's mother and his marriage to third wife Judith Nathan.
"There's obviously a little problem that exists between me and his wife," Andrew Giuliani told The New York Times earlier this year.
On Monday, he told ABC News: "That story was overdone. It was nowhere near as bad as the story made it sound."
Asked about his sister's possible support for Obama, Andrew Giuliani said: "I love my sister very much and I respect her opinions. One of the great things about our parents is they've always encouraged us to see the world for ourselves."
In May, Rudy Giuliani attended his daughter's high school graduation but kept a low profile, sitting in a last-row balcony seat with his wife and leaving without speaking to his daughter, the New York Daily News reported.
Andrew previously told The New York Times that he would be too busy working on his golf game to participate in his father's presidential campaign.
"It's not the first time children of a presidential candidate have been estranged personally or politically from their parent," said CBSNews.com Senior Political Editor Vaughn Ververs. "Rudy Giuliani's bitter, and very public, divorce from Donna Hanover — mother of Caroline and Andrew — has left some very visible scars which won't make social conservatives within the Republican Party any more comfortable with his candidacy, but is unlikely to be a decisive issue."