The Stratford, Ont. singer posted a note via Twitter Wednesday night acknowledging that he had spoken to Clinton.
"[T]hanks for taking the time to talk Mr. President. Your words meant alot," the 19-year-old Bieber wrote.
The message has since been removed from the singer's list of public posts.
An earlier Wednesday message read: "In life u will make mistakes and people will try and tear u down...but u gotta stay positive. Stay strong..and learn to be better."
Earlier this week, gossip website TMZ posted a video it claimed showed the Canadian singer and his entourage exiting a nightclub through its kitchen.
In the poorly shot footage, a young man is seen urinating in a janitorial bucket to the laughter of his companions. He is also shown grabbing what appears to be a bottle of cleanser, spritzing an image of the former president on display and hurling the expletive declaration, "F--k Bill Clinton."
As he traverses the globe on his Believe world tour, the Canadian singer, who turned 19 in March, has made headlines internationally for outrageous antics (late concert starts, scuffles with paparazzi and reckless driving around his home), controversial actions (leaving a questionable note at the Anne Frank Museum or abandoning his pet monkey in Germany) or simply bizarre behaviour (gallivanting topless).