"The Pope did not enter into the details of the situation of Mrs. Davis, and his meeting with her should not be considered a form of support of her position in all of its particular and complex aspects," Vatican spokesman the Rev. Federico Lombardi said in a statement issued Friday morning.
The meeting, on September 24 at the Vatican Embassy in Washington, added a political twist to the Pope's first-ever trip to the United States, with conservatives cheering and liberals puzzled.
Davis' lawyer, Mat Staver, had said the audience lasted 10 minutes and was just between the Pope
, his client and her husband. Lombardi disputed that account, saying "several dozen" people were present at the Vatican Embassy during the meeting.
"Such brief greetings occur on all papal visits and are due to the Pope's characteristic kindness and availability. The only real audience granted by the pope at the nunciature (embassy) was with one of his former students and his family," Lombardi said.
Earlier this week, Davis had framed the meeting as an endorsement of her cause, telling ABC News: "Just knowing the Pope is on track with what we're doing, and agreeing, you know, kind of validates everything."
In a statement, Davis added: "Pope Francis was kind, genuinely caring, and very personable. He even asked me to pray for him. Pope Francis thanked me for my courage and told me to 'stay strong.' "
Staver, who didn't attend the meeting, said the Pope hugged Davis and gave her and her husband each a rosary, which she in turn gave to her parents. Rosaries are common gifts from popes to visitors.
Davis' father and mother are lifelong Catholics. She is an Apostolic Christian after a religious conversion four-and-a-half years ago.
Initially, the Vatican barely acknowledged the meeting.
"I don't deny that the meeting took place," said Lombardi. "But I have no comment to add."
The meeting added a partisan wrinkle to Pope Francis' trip last week.
While he strongly defended religious freedom in speeches at the White House, Congress and Philadelphia's Independence Mall, he avoided taking public stances on particular political issues.
Davis, meanwhile, personifies religious conservatives' concerns about the enforcement of nondiscrimination laws.
Gay and lesbian Catholics called the Pope's meeting with Davis "puzzling"
and said it "throws a wet blanket" on his trip to the United States last week.
While in Washington last week, Francis also met with the Little Sisters of the Poor, nuns who are suing the Obama administration over the Affordable Care Act's contraception mandate. That meeting, too, took place behind closed doors.
A federal judge ordered Davis to jail this month over her refusal to issue marriage licenses to same-sex couples in the Kentucky county where she's clerk. Before being ordered to jail, Davis also refused to allow clerks in her office to issue licenses. She cited her biblical opposition to same-sex marriage
Since her release, she has allowed the licenses to be issued, but only with her name and title removed. Each license includes a statement saying it is issued "pursuant to a court order."