The court kept in mind that Roy 'is a woman'
Ms Roy received the sentence after being found guilty of contempt of court.
If she had refused to pay the fine, her jail term would have been extended to three months.
India's Supreme Court made the judgement against the author in connection with remarks she made about a legal decision to allow work on the controversial Narmada Dam project.
After her release, Ms Roy told reporters: "The fine was not in lieu of an apology. The fine was a punishment.
"I am obviously appalled by the verdict and I stand by everything I said."
Ms Roy took part in a demonstration in December to underline her opposition to the court's decision to allow the resumption of work at the dam.
She was supported by other environmental campaigners, including the leading anti-dam activist Medha Patkar.
The court issued a notice to the writer for making what it considered disrespectful remarks at the time about its ruling in relation to the dam.
'Symbolic' imprisonment
A two-judge bench of the Supreme Court ruled that "freedom of speech is subject to reasonable restrictions" and that the court's sanctity had to be maintained.
They said they were handing out a symbolic imprisonment to demonstrate that the court could be magnanimous, and had kept in mind that Ms Roy was a woman.
"I stand by what I said. I am prepared to suffer the consequences," the author said as she was taken to Delhi's Tihar Jail.
Arundhati Roy had criticised the Supreme Court's judgement in the Narmada issue and accused it of trying to silencing dissent and harassment.
As she appeared in court on Wednesday, her supporters stood outside.
"This will definitely take our campaign to a much higher level," said Medha Patkar, who heads the anti-Narmada dam campaign.
This is the third time the 1997 Booker Prize winner has been issued a notice in this case.
Last year, the court did not take further action against Ms Roy for writing critical articles on issues surrounding the Narmada Dam, which included strong criticism of judicial proceedings.
Over the years, the Narmada dam project has attracted a great deal of controversy, with critics questioning its promised benefits at the cost of large-scale human displacement.