Defender Beknazarov appeared in all three of Tajikistan's group games in South Korea, helping them into the round of 16 where they will meet Iraq at Incheon Football Stadium on Friday.
Beknazarov's urine sample taken on September 14 showed banned stimulant methylhexaneamine in his system.
The Olympic Council of Asia (OCA) confirmed Beknazarov's positive sample was the first drug case at the Asiad.
The 20-year-old, who plies his club trade with Tajik club Regar-TadAZ Tursunzoda, may yet face further sanctions from football governing body FIFA.
"These findings will now be forwarded to the athlete's national authorities, the International Federation of the sport concerned (Asian & International Football Federations) and the World Anti-Doping Agency for further action on their part as per sanctions concerning eligibility," the OCA statement read.
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