But the girls` parents had accused the Central Bureau of Investigation (CBI) of "trying to fudge the case".
Rights groups and their relatives said many questions remained unanswered.
The lower-caste cousins, thought to have been 14 and 15, were found hanged from a mango tree on 28 May 2014 in Uttar Pradesh.
The initial reports that the girls had been gang-raped and murdered by a group of men from the same village sparked global outrage.
A local post-mortem examination initially confirmed multiple sexual assaults and death due to hanging.
`Closure report`
But in December, the CBI filed a "closure report" in court, saying investigators had studied "around 40 scientific reports" and "questioned over 200 people" and come to the conclusion that the elder girl had "an intimate relationship" with one of the three men and that the other girl, her younger cousin, was "facilitating the relationship".
The girls killed themselves after they were found by a neighbour and because they were afraid of facing their families, the report added.
It accused the families of filing a false complaint of rape and murder and requested that the case be closed.
The girls` relatives accused the CBI of conducting "a shoddy investigation" and filed a "protest petition" in a local court in Badaun town.
On Wednesday, the special court that deals with cases of sexual offences against children rejected the CBI report and also summoned the main suspects in the case to the next date of hearing.
A CBI spokesman said they were yet to get the detailed court order and would comment only after studying it, the Indian Express newspaper reported.
Three men arrested in connection with the case and two policemen accused of "dereliction of duty" were freed on bail in September.
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