After days of confusion, a statement has been issued clarifying Francis's meeting with Mrs Davis, a county clerk in Kentucky who refuses to sign marriage licences for gay couples.
The Vatican said Pope Francis met with many people during his US visit, due to his "kindness and availability".
The statement said: "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."
Mrs Davis, a Rowan County clerk, spent five days in jail for defying a series of federal court orders to issue same-sex marriage licences.
She said earlier this week that she and her husband met briefly with the pope at the Vatican's embassy in Washington and that he encouraged her to "stay strong".
She later said in an interview: "Just knowing that the pope is on track with what we're doing and agreeing, you know, it kind of validates everything."
News of the audience quickly spread through the US church, with Mrs Davis's supporters saying it showed the pope backed her cause.
However, her opponents questioned whether the pope had been duped into meeting with her and truly knew the details of her case.
Mrs Davis' cause seemed to be given extra weight when the pontiff declared on his flight back to Rome that conscientious objection was a "human right".
He said: "It is a right. And if a person does not allow others to be a conscientious objector, he denies a right."
The Vatican statement made clear the pope expressed no such sentiments.
Initially the Vatican only reluctantly confirmed the meeting but offered no comment.
Meanwhile a poll in Kentucky has revealed a split of opinion over Mrs Davis' stance.
It suggests that 51% of people believe she should be required to issue the forms, while 42% think she should have the freedom to refuse.
Seven per cent said they were not sure which position they agreed with.