Sunanda Pushkar was found in a hotel room in the Indian capital, Delhi, on Friday.
The couple became embroiled in a row on Wednesday after Twitter messages suggested he was having an affair.
The autopsy also found "injury marks" on Ms Pushkar's body, but did not say if they were linked to her death.
Dr Amit Gupta, spokesperson of Delhi's All India Institute of Medical Sciences, where the autopsy was conducted, told the BBC that the "preliminary report shows there was drug overdose".
The autopsy report has been submitted to a magistrate, media reports say.
A public row broke out on Wednesday when seemingly private messages between Mr Tharoor and Pakistani journalist Mehr Tarar were published on his Twitter feed.
Ms Pushkar, 52, said she had gone into her husband's account and published the messages.
She accused Ms Tarar of stalking her husband - an allegation denied by the Pakistani journalist.
Ms Pushkar and Mr Tharoor later insisted they were happily married and blamed "unauthorised tweets" for causing confusion.
Mr Tharoor, a former UN diplomat, was forced to resign from his first ministerial position in 2010 amid controversy over his involvement in bidding for a cricket team.
Ms Pushkar had allegedly received a free stake in the Indian Premier League franchise he was bidding for.
He was appointed minister of state for human resource development in 2012.
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