But the court said the National Investigation Agency (NIA) would continue its probe into the criminal dimension of the case, if any.
"We clarify that the investigation by the NIA in respect of any matter of criminality may continue in accordance with law," the court said.
Pronouncing a brief operative order after lunch, Chief Justice Misra said the high court should not have annulled the marriage, following a Habeas Corpus petition, by exercising its powers under Article 226 of the Constitution.
The order also referred to Hadiya personally appearing before the Supreme Court on November 27 and admitting to her marriage with Shafin Jahan, who had challenged the High Court order that nullified the marriage.
Hadiya, 24, embraced Islam and married Shafin Jahan, a Muslim. Hadiya's father alleged that she was forcibly converted by groups with links to terrorist outfits.
In the course of the arguments on Thursday, senior counsel Kapil Sibal, appearing for Shafin Jahan, submitted nine propositions of law to be addressed before looking into the case on facts.
He said that the right to choose a life partner is part of right to life and the marriage can only be dissolved by any one of the two in wedlock.
Asserting that in certain cases the high court can annul a marriage, senior counsel Shyam Divan, appearing for Hadiya's father Asokan K.M., said "Hadiya's marriage with Shafin Jahan was to defeat the proceedings before the high court".
Observing that they (the couple) can't go without the passport and the government had powers to prevent them from leaving the country, the court asked if NIA investigation has found any offence against the couple.
The court made it clear that the NIA could continue with its investigation but without interfering in their married life.
On October 3, the Supreme Court had said it would examine whether the high court could annul the marriage following a petition by her parents.
Reacting to the Supreme Court verdict on Thursday, Hadiya's father said he "respects the court order but will seek legal recourse on the verdict".
"The verdict has only cleared that her marriage is in order. The court has asked for the NIA probe to continue as the larger question we raised is that Shafin Jahan is a terrorist," he told the media at his house near Kottayam in Kerala.
"We accept the apex court's order as the law has to be respected. A father is in pain to hear that his daughter has gone with a terrorist. We still maintain the marriage was stage-managed... We will seek legal recourse," Asokan said.
(This story has not been edited by Business Standard staff and is auto-generated from a syndicated feed.)