Ehsan Jafri was among 69 people killed burnt alive by a mob during the riots at Gulburg Housing Society here on February 28, 2002.
Metropolitan Magistrate B J Ganatra ruled that Jafri cannot file the protest petition as she failed to file it despite being given sufficient time.
The court ruled that Jafri can now only make oral submission regarding her protest against the SIT report.
The court order comes at a time when the state is in midst of assembly poll campaigning and Modi is seeking a fourth term as Chief Minister of Gujarat.
The SIT had submitted its final report in the court regarding Gulburg Society riot case giving a clean chit to Modi and others in 2002 riot cases in February.
The SIT had provided a copy of the report to Zakia in May asking her to file a protest petition within the stipulated time of two months. However, the protest petition has not yet been filed by Jafri.
Jafri's lawyer S M Vohra told the court that they have approached the Supreme Court seeking a clarification on certain issues and the next date of hearing of the case in the apex court is December 3.
Vohra sought time from the court till the hearing in the case is over in the Supreme Court.
Vohra later said that generally local courts await the outcome of the case in the Supreme Court. However, this court has chosen not to wait for the same and given an order which is "very shocking."
"We will convey this to the Supreme Court before December 3," Vohra said.
Vohra said, "we protested in the court against the order". The SIT was formed by the Supreme Court to investigate Zakia Jafri's allegation that Modi, other ministers of his cabinet, police officers and members of some right wing organisations were behind the larger conspiracy of the 2002 riots in which more than 1,000 people were killed.
The SIT had submitted its report to the Supreme Court giving a clean chit to Modi and others after investigations.
It had interrogated Modi for over nine hours as also many others in connection with the case.
The Supreme Court had, after going through the report, asked amicus curie Raju Ramchandran to independently verify the SIT investigations. Ramchandran had also submitted his report to the Supreme court.
The apex court had directed the SIT on September 12, 2011 to forward the report to the local court.