Abdullah bin Mohammed al-Sheikh, the Saudi justice minister, told Al Jazirah daily that the pardon does not mean the king doubted the country's judges, but instead acted in the "interests of the people".
The girl's sentencing had triggered international outrage.
"The king always looks into alleviating the suffering of the citizens when he becomes sure that these verdicts will leave psychological effects on the convicted people, though he is convinced and sure that the verdicts were fair."
The victim's husband welcomed the news, but said he had not been informed officially of the pardon decree.
"I am happy and my wife is happy and it will of course help lift some of her psychological and social suffering," he told the Reuters news agency.
"We thank the king for his generous attention and fatherly spirit."
Increased sentencing
The girl and a man were in a car when they were kidnapped and raped at knifepoint by seven men in 2006.
The girl, who was 18 at the time of the rape, was originally sentenced to 90 lashes in October 2006 for being alone with the man - which is against the Saudi's strict interpretation of Islamic law.
The rapists were sentenced to between one and five years.
The Supreme Judicial Council increased the girl's sentence to 200 lashes and six months in jail last month after she appealed, saying she had attempted "to aggravate and influence the judiciary through the media".
The rapists also had their sentences increased to between two and nine years in November.
US reaction
In Washington, Dana Perino, the White House spokeswoman, welcomed the move, saying: "This is a decision that King Abdullah needed to make on behalf of Saudi Arabia, and we think it was the right one."
George W Bush, the US president, said earlier this month that King Abdullah "knows our position loud and clear" on the case.
Waheed Hamzah Hashem, a professor at King Abdul Aziz University, told Al Jazeera that the king can intervene if it serves the interests of the people.
However, he cautioned: "Don't think he acted because he felt the pressure of the international outcry.
"He acted because he felt that in this specific case there was some misunderstanding or misinterpretation by the judge and therefore he has to intervene in order to achieve justice for all."