The court said that as a principle, marital disputes involving a converted Muslim spouse and a non-Muslim partner should only be decided in a civil court and not in the sharia court.
But at the same time, the court said Subhasini's husband has the right to approach the shariah court to seek redress.
Civil-rights groups have voiced fears that minority rights have become subordinate to Islamic jurisprudence because of a series of rulings that have gone in favour of Muslim spouses.
Nik Hashim Nik Abdul Rahman, one of the two judges who dismissed the case, said: "The civil and sharia courts cannot interfere with each other's jurisdiction."
There was one dissenter.
Controversal family law
Family law is a controversal area in Malayia's courts. Non-Muslims complain that civil courts give up their responsbilty to their Islamic counterparts too easily in cases involving a Muslim conversion.
In Malaysia marriages between Muslims and non-Muslims are forbidden.
Therefore, once a spouse converts to Islam, the union is broken in the eyes of Islamic courts.
K Shanmuga, Subashini's lawyer, said the judges' comments made it clear they recognised the husband's right, as a newly converted Muslim, to have recourse to the Islamic courts.
In summing up the ruling's significance Shanmuga said: "The high court has jurisdiction to hear matters when this is a non-Muslim marriage but the husband also has a right to sharia court under Islamic law."
In the civil court Shanmuga cited a landmark ruling by the federal court in July which stated that if one party was a non-Muslim, the sharia court had no jurisdiction.
This was a rare ruling that went against a tide of decisions granting jurisdiction to the Islamic courts.