The general is hoping to legitimise his rule after seizing power in a coup in 2021.
A civil society group calling for the return of civilian rule has condemned the election as a "charade" after Gen Doumbouya's main rivals were barred from contesting, while opposition candidates said the poll was marred by irregularities.
The Democratic Front of Guinea's flagbearer, Abdoulaye Yero Balde, came a distant second with 6.6%, followed by the Liberal Bloc's Faya Lansana Millimono with 2%, provisional results show.
On Monday, internet monitoring group NetBlocks reported that access to social media platforms TikTok, YouTube and Facebook had been restricted as Guineans waited for the full results.
There has been no official comment on the restrictions, but opponents see it as an attempt by the junta to stifle criticism of the results.
The 41-year-old general's victory gives him a seven-year mandate. Should the results be challenged, the Supreme Court has eight days to validate them.