"The court has no choice but to declare that Siti Fatimah Tan Abdullah is no longer a Muslim as she has never practised the teachings of Islam," Othman told a packed courtroom on Wednesday.
"I order the conversion certificate to be nullified," he added.
Siti Fatimah or Tan Ean Huang, 38, said she had never practised Islam since she converted in 1998 and only did so to enable her to marry Iranian Ferdoun Ashanian.
State council failure
The couple married in 2004 but since then her husband has left her following which she filed for the renunciation.
Othman said it was clear from witnesses and the evidence presented that Siti had continued to practise Buddhism even after her conversion.
He rebuked the state council for not counselling and looking after the welfare of new converts.
"In this case, it is clear that the council has failed to live up to its responsibilities and the outcome is clear for all to see," he said.
Siti said she was happy with the court's decision.
"I'm relieved that the matter is finally settled after two years, and I am now looking forward to doing something with my life again," she said.
The court's verdict comes amid racial and religious tensions in multiracial Malaysia, where minority religious groups fear their rights are being undermined, even though the country is traditionally seen as moderate.