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The high court's Justice Sonia Gokani, while rejecting Ms Jafri's allegations, said she can move higher forums or the Supreme Court against today's ruling.
Zakia Jafri, 79, had approached the high court in March 2014 against a lower court verdict accepting the SIT's report, which concluded that then Chief Minister Modi took all possible steps to control the riots that swept through Gujarat after coaches of the Sabarmati Express train were set afire at Godhra station in the state, killing 59 people.
The petition filed by Zakia Jafri and the NGO Citizen for Justice and Peace, run by Teesta Setalvad, alleged that the then Chief Minister had turned a blind eye to the violence and had sought a criminal trial against PM Modi and 58 others.
Justice Gokani had started final hearings in the case in 2015. The SIT's lawyer defended its findings, underlining that these have already been reviewed by the top court's amicus curiae, or friend of the court.
The SIT report, filed in 2012, had said no charges made by Zakia Jafri were maintainable and had questioned the motive behind her filing her complaint four years after the riots. In 2013, the lower court rejected Ms Jafri's petition against the report and she moved the high court.
The massacre at Gulbarg Society - a cluster of 29 bungalows and 10 apartment buildings housing mostly Muslims - was among the 10 major Gujarat riot cases re-investigated by the special team appointed by the Supreme Court.
Ehsaan Jafri, a former Congress parliamentarian, was among 69 people dragged out, hacked and burnt by the rioters. The Congress leader's frantic phone calls to police officers and senior politicians for help went unanswered, Zakia Jafri has alleged.
Last year, a special court in Ahmedabad convicted 24 attackers for the massacre that the court described as the "darkest day in the history of civil society." But the court, which also acquitted 36 people including a BJP corporator in this case, underlined that there was no larger conspiracy.
The verdict was seen as another setback for the Jafris, who alleged that people involved in the massacre were allowed to get away. "They must get the punishment as they killed people and destroyed their families. I saw them doing it with my own eyes," Ms Jafri said.
The trial court had ruled that Mr Jafri opening fire in self-defence had "acted as a catalyst and infuriated the mob".