The alleged incident happened in the early hours of Dec. 30, when the limousine picked up six people including Bieber, 19, outside a Toronto nightclub, police said in a statement.
Bieber allegedly struck the limousine driver on the back of the head several times during an altercation on the way to a hotel, police said. The driver got out and called police, but Bieber left before they arrived, according to the statement.
A Canadian lawyer for the pop star issued a statement that said Bieber is innocent.
"As the matter is now before the court, it would be inappropriate to address the specifics of either the allegation or of the defence at this time," it said.
Bieber's legal team expects the matter will be treated as a summary offence, the equivalent of a misdemeanor in the United States.
The pop star is scheduled to appear in a Toronto courtroom on March 10.
Bieber was charged after appearing at a Toronto police station on Wednesday evening (local time). He arrived in a black SUV and was met by a crowd of journalists and screaming fans, who braved temperatures of minus 10 Celsius (14 Fahrenheit).
Wearing a baseball cap on backwards and hooded black coat, Bieber was mobbed by photographers and fans pushing for a closer look as bodyguards and police officers cleared a path for him to enter the station.
FACING FLORIDA CHARGES
Bieber has also been in trouble with authorities in the United States this month. He was charged with driving under the influence in Miami after police say he was caught drag racing a rented Lamborghini. Police said Bieber told them he had taken prescription medicine, smoked marijuana and consumed alcohol.
According to court records, he pleaded not guilty on Wednesday to those charges. If convicted, Bieber could face up to six months in prison, although experts say he is likely to receive a lighter sentence because it would be his first offence.
Bieber is scheduled to make a court appearance on Feb. 14 to formally answer those charges. He was also charged with driving on an expired license and resisting arrest.
Also on Wednesday, an online petition asking the administration of President Barack Obama to deport Bieber from the United States following his Miami arrest passed the 100,000-signature threshold required for a White House response.
Bieber is unlikely to be deported because federal law dictates that a visa can only be revoked or denied for a conviction of a violent crime with a minimum one-year prison sentence.
Bieber, a native of Ontario, Canada, first shot to fame as a child when his mother posted YouTube videos of him singing. He became a musical and social media sensation with a devoted following of young, mainly female fans.
The "Boyfriend" singer's life off-stage has been rocky in the last year with problems ranging from scuffling with paparazzi in London to a felony investigation into whether he pelted a neighbor's house with eggs in his gated community near Los Angeles.
But the recent charges and other problems have not dented his appeal with some fans, including those gathered outside the Toronto police station on a chilly Wednesday night.
A 24-year old Toronto woman, who identified herself only as Chantal, said when she heard about the appearance she came out to show her support.
"I know he makes mistakes but I'll always be a fan," she said. "He's a 19-year-old guy. I mean every 19-year-old or teenager goes through the same struggles. It's just not amplified and it's just not shown to everyone."
"We support you. Your Beliebers love you," she added.
