The top court, however, clarified that the National Investigating Agency (NIA) may go ahead with the investigation in respect to any criminality.
In Kochi, Hadiya's father K M Asokan said he would consider moving a review petition in the Supreme Court against its judgement.
He maintained that his daughter's marriage with Shafin Jahan was an act of "adjustment" done by a group.
A bench of Chief Justice Dipak Misra said that the high court should not have annulled the marriage between Hadiya alias Akhila Asokan and Shafin Jahan by its order dated May 24, 2017 in a habeas corpus petition.
The top court said it had directed the personal appearance of Hadiya on November 27, last year and she had admitted her marriage with Jahan.
"In view of the aforesaid, the appeal stands allowed. The judgement and order passed by the high court is set aside. Respondent No.9, Hadiya alias Akhila Asokan is at liberty to pursue her future endeavours according to law," it said and added that NIA can continue its investigation.
Earlier during the day, the apex court clarified that a court cannot interfere in the marriage of two consenting adult and cannot annul the marriage in a habeas corpus (a writ requiring a person under arrest to be brought before a judge or into court, for securing the person's release) petition.
It had said that Article 226 gives the extraordinary power to the high courts to protect the constitutional right not to scuttle it.
He said that high court had no jurisdiction to annul the marriage and it can be challenged only by the party to the marriage but no third party can interfere in it.
"The jurisdiction of marriage is not in the marriage of consenting adults and no investigating agency can interfere in the marriage. Even the father of girl can't interfere," Sibal argued.
Senior advocate Shyam Divan, appearing for Asokan, said that the high court was right in annulling the marriage and it has inherent jurisdiction under Article 226 of Constitution.
The bench said that a court cannot interfere where there is free consent between the adults and it has called Hadiya and talked to her.
Divan said that this marriage of Hadiya was in an exceptional circumstances and the court was right in interfering in it as it can't loose the oversight of a 'vulnerable adult'.
Divan added that high court found that there was a well oiled machinery working to use the marriage of Hadiya as a guise to put the matter out of the court's reach.
Additional Solicitor General Maninder Singh, appearing for the NIA, said that its investigation in the case is over and look out circular has been issued against two persons who are suspected to have gone out of the country.
"You (NIA) can carry out the investigation with regard to the offences but you cannot touch the marriage. Investigate anything but marriage", the bench said.
The apex court said that it will pass detailed verdict in the petition at a later stage.
The apex court had in August last year asked the NIA to probe the case of conversion and marriage of Hadiya, as the agency claimed a "pattern" was emerging in Kerala.
The matter came to the fore when Hadiya's husband Shafin Jahan challenged a Kerala High Court order annulling his marriage and sending her to her parents' custody.
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