The court however rejected the investigating agency CBI's appeal seeking death penalty for three of the convicts.
A division bench of Justices V K Tahilramani and Mridula Bhatkar in its 430-page judgement said while the probe conducted by Gujarat police was "flawed with a dishonest investigation", the evidence and statements given by Bilkis Bano were "completely trustworthy".
Bilkis, who was gang-raped in March 2002 during the post-Godhra riots in Gujarat when she was pregnant, said in her reaction that her rights as a woman and a mother had been violated in the most brutal manner, and the verdict "vindicated truth" and confirmed her faith in the judiciary.
"The appeal against conviction filed by the 11 convicts (one convict is dead) is dismissed. The conviction and sentence is upheld. The appeal filed by the prosecution against the acquittal of seven persons is allowed. The acquittal is set aside," the court said.
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The HC convicted seven persons -- five policemen and two doctors -- under section 218 IPC relating to public servant framing incorrect record or writing with intent to save person from punishment or property from forfeiture and 201 for tampering with evidence.
"We will consider the period undergone in jail of these seven persons as their sentence. But we will impose fine on them," the court said.
Those convicted are policemen Narpat Singh, Idris Abdul Saiyed, Bikabhai Patel, Ramsingh Bhabhor and Ramanbhai Bhagora, and doctors Arun Kumar Prasad and Sangeeta Kumar Prasad.
"We are convinced that all these accused persons in a mob on account of the Godhra incident were moving in search of Muslims," said the High Court.
"This is a case where the police wanted to help the accused by suppressing their names. The police were not passive towards investigation but they were very active in destroying the case of the prosecutrix (Bilkis)," it said.
"They (police) wanted to screen the perpetrators of the crime for the reasons best known to the police. This is how they gagged mouth of the prosecutrix so that her cry for justice would not be heard by anybody," the judges said.
Bilkis was the only witness on whose testimony the entire case of the prosecution stood, the court noted.
"The case in fact suffers at the starting point with the first major flaw of dishonest investigation," the bench said.
"I am happy that the state and its officials who emboldened, encouraged, and protected the criminals who destroyed the life of an entire community, are no longer unblemished and today stand charged with tampering of evidence.
"For officers of the state, whose sworn duty is to protect citizens and enable justice, this should be their great moral shame, to bear forever," the statement said.
A special court in Mumbai had on January 21, 2008 convicted and sentenced twelve men to life imprisonment. One of them died subsequently.
According to the prosecution, on March 3, 2002, Bilkis Bano's family was attacked by a mob at Randhikpur village near Ahmedabad during the post-Godhra riots and seven members of the family were killed.
Bilkis, who was five months pregnant, was gang-raped, while six others of her family managed to escape.
The trial began in Ahmedabad. However, after Bilkis expressed apprehension that witnesses could be harmed and evidence tampered with, the Supreme Court transferred the trial to Mumbai in August 2004.
The convicts had challenged the verdict claiming CBI had fabricated the evidence, that Bilkis gave birth to a child after the incident so she could not have been gang-raped, and investigators' failure to find the bodies of some of her family members proved they were not killed.
The CBI had sought death sentence for Jaswantbhai, Govindbhai and Radhesham Shah on the ground that they had raped Bilkis.