The pop star also had repercussions from a tour stop in Chicago earlier this week when city officials said Bieber was listed as an underage guest on a citation that police issued to a nightclub.
Clinton's office said on Thursday the pop star called and "he apologised and offered to help the Clinton Foundation".
Clinton's office declined to provide any other details.
A video released Wednesday by TMZ.com shows the 19-year-old Bieber urinating in a mop bucket as he and others race through the restaurant kitchen.
Before exiting, Bieber sprayed the Clinton photo and dropped the F-bomb in reference to the former president.
Bieber tweeted to his more than 41-million followers Wednesday night, thanking Clinton "for taking the time to talk."
Bieber tweeted: "Your words meant alot. #greatguy."
Separately, Chicago department of business affairs and consumer protection spokesperson Jennifer Lipford confirmed on Thursday that the 19-year-old Bieber was listed as an underage guest on a citation of Bodi nightclub.
Police cited the club early on Wednesday for admitting and knowingly having an underage person in the establishment, she said.
Bieber performed in a concert at Chicago's United Center on Tuesday evening. The next step is for the citation to go to an administrative hearing. The club faces a fine of up to $1 000. A date hasn't been set.
Bodi issued a statement saying Bieber made a brief appearance to support a friend who is a DJ and was performing at the nightclub. The club said Bieber was not served alcohol.
"Neither Justin nor anyone affiliated with Bodi broke any laws," the statement said. "We believe this matter amounts to a simple misunderstanding with local police officers."
A representative for Bieber did not immediately have comment. – Sapa-AP