The verdict was accompanied by scathing remarks questioning the intention of petitioners, underlining that political rivalries had to be resolved in the great hall of democracy, not courts. Soon after, Law Minister Ravi Shankar Prasad demanded an apology from the Congress president for, what he called, was an effort to settle political scores through the court.
The petitioners had "acted as a front of the Congress or in association with the Congress", Mr Prasad said. BJP spokesperson Sambit Patra had gone a step ahead, insisting Rahul Gandhi's "invisible hand" was behind this petition.
"Now what do you have to say," the law minister had asked Mr Gandhi, demanding an apology and reaction to the court verdict.
Mr Gandhi tweeted his response, suggesting that people instinctively knew the truth about the case irrespective of the court's conclusion.
"Indians are deeply intelligent. Most Indians, including those in the BJP, instinctively understand the truth about Mr Amit Shah. The truth has its own way of catching up with people like him," tweeted Mr Gandhi.
Judge Loya, 48, was hearing the Sohrabuddin Sheikh fake encounter case, in which Amit Shah was an accused when he died on 1 December 2014. The judge who replaced him had cleared Amit Shah in the case days later.
But it was only last year that questions were raised about the death after the judge's sister Anuradha Biyani questioned the circumstances of his death in an interview to the Caravan magazine. Another relative alleged that the judge was offered a huge bribe and was under immense mental pressure.
The case became a rallying point for the opposition, which said there was a threat to democracy when lawyers and judges working on important cases were targeted.
Sitaram Yechury of the CPM had called the top court's verdict "unfortunate" and sought a review by a larger bench while the Congress listed 10 questions that the ruling had left unanswered, saying it marked a "sad day" in the country's history.