They have been summoned to appear in court on February 28.
CBI Special Magistrate Preeti Singh passed the ruling against the couple, paving the way for the trial.
Aarushi and the family's domestic help Hemraj were killed in May 2008.
The CBI had on December 29, 2010 filed for closing the case, saying that Rajesh was the sole suspect in the case but there was no conclusive evidence against him. Rajesh contested this and asked for a copy of the closure report but his request was denied.
Rajesh had also submitted a 90-page rebuttal against the closure report.
The CBI magistrate ruled that the trial of the Talwars will be held under sections 120B (criminal conspiracy), 302 (murder), 201 (disappearance of evidence of offence) and 34 (criminal acts by several people) of the Indian Penal Code.
Shocked
Nupur Talwar said: "It is a very unfortunate judgment. We will challenge this judgment in the superior court. The court has not looked into our 90-page protest petition."
Rebecca John, the couple's lawyer, said the family was shocked after learning about the order.
"We will challenge the order and go to a higher court. We were surprised by the CBI closure report as it was full of such gaping holes," she said.
"We are definitely taken aback by the order. Nothing can justify the summoning of Rajesh Talwar [for the next hearing] but having done it, we will go to higher court challenging the order," she added.
Raising a question on the investigative agency, John said: "This was the present team which is saying it. The CBI, about a year-and-a-half back, said completely different thing. They hid the investigation done by the previous team of the CBI.'"
Reacting to the developments, senior lawyer Khalid Khan said: "The court judgment is landmark and appreciable. The court has taken cognisance on the facts furnished."
‘In this case, the court has taken cognisance after rejecting the closure report,' he added. Special Magistrate Singh was told by the probe agency that it had not found any substantial evidence in the case and a closure report was its only option.
"The fingerprints found on a [blood stained] wall also could not be verified by the forensic lab," CBI lawyer R.K. Saini had told the court.
Aarushi, 14, was found murdered under mysterious circumstances in her parents' Jalvayu Vihar apartment in Noida on May 16, 2008. Their domestic help Hemraj was initially suspected for the killing, but his body was found on the flat's terrace a day later.
Talwar was arrested soon after the murders but was released when investigators could not find evidence.
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