The 35-year-old, who played the last of his 57 one-day internationals in 2012 but has been active in domestic cricket, "inadvertently ingested" a prohibited substance to treat an upper respiratory tract infection, the BCCI said in a statement on Tuesday.
A urine sample collected last year tested positive for terbutaline, which features in the World Anti-Doping Agency's list of prohibited substances.
He was provisionally suspended in October and the board, convinced by the player's explanation, backdated the start of his five-month suspension to mid-August.
News that makes sense
Your trusted source for staying up-to-date with the world around you. Get free daily news updates and analysis, straight to your inbox.
"Having considered all of the evidence and taken expert external advice, the BCCI has accepted Mr Pathan's explanation ... and on that basis has agreed that a period of ineligibility of five months should apply, together with the disqualification of certain results."
Pathan, whose six-hitting ability and tidy off-spin bowling made him a limited-overs asset, is free to play from Monday.
(Reporting by Amlan Chakraborty in New Delhi; editing by Peter Rutherford)
