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 between the two, 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.
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.
Hadiya, 24, earlier Akhila Ashokan, embraced Islam and married Shafin Jahan, a Muslim. Hadiya's father alleged that she was forcibly converted by groups with links to terrorist outfits.
Reacting to the Supreme Court verdict on Thursday, Hadiya's father Ashokan 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," Ashokan added.
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