The CBI petition comes just days after Attorney General KK Venugopal advised the government against an appeal, saying it was likely to be dismissed only on account of the long delay.
Sources say Mr Venugopal changed his mind and gave CBI the thumbs up after its officials showed him fresh documents.
The top government lawyer had earlier advised the investigating agency to remain a respondent in the case filed by Ajay Kumar Agrawal, a BJP member and advocate, who last year challenged the high court judgment in the Rs 64-crore Bofors scandal.
Mr Venugopal reasoned in a note that if the CBI’s separate petition was dismissed in the Supreme Court, it would prejudice the case.
But the CBI was reportedly keen to file the appeal and there were reports that its officers had told a group of lawmakers that they had the evidence to back up their petition.
The 1986 Bofors howitzer gun deal devastated the Congress government of Rajiv Gandhi and ruined the party's prospects of returning to power for several years.
The Bofors case revolved around allegations that Swedish defence manufacturer Bofors paid huge kickbacks to former prime minister Rajiv Gandhi and others for the sale of its artillery gun to India.
The High Court said there was no evidence that Rajiv Gandhi had accepted bribes. Rajiv Gandhi - Sonia Gandhi's husband and Rahul Gandhi's father - was assassinated in 1991.
Last October, the CBI had indicated that it was considering an appeal against the High Court decision after Michael Hershman, a private detective from US-based firm Fairfax, alleged that the Rajiv Gandhi government had sabotaged his investigation into the case.
In the first hearing of Ajay Kumar Agarwal's appeal earlier this month, the Supreme Court had wondered why the court should go into it when the appeal hadn’t been filed by the prosecutor in the case, the CBI. The top court was to take up the case today but had to defer the hearing.