The 26-year-old tested positive for benzoylecgonine, a metabolite of cocaine, after Thistle's Premiership match against Celtic on 3 December last year.
He was banned for two years in April by the National Anti-Doping Panel.
Following an appeal by McMillan, the NADP reconvened in Glasgow in July and upheld the original decision.
McMillan's suspension runs from 18 December 2014 to 17 December 2016.
The player does not deny the validity of the test but has always said he consumed the cocaine without knowing he had done so.
McMillan says that, while at the home of his partner's parents, he drank from the wrong glass, not realising the drink had been mixed with cocaine by a friend of his partner's family, who had tried to hide his drug consumption.
McMillan's agent, Tony Asghar, told Ukad: "He was oblivious to the fact that it contained any other substance [than alcohol] and thought nothing of it."
Ukad chief executive Nicole Sapstead stressed the importance to all athletes of "strict liability".
She said: "They are solely responsible for any banned substance that is found in their system, regardless of how it got there or whether there was an intention to cheat or not.
"The principle of strict liability can be challenging for athletes. They have to ensure that they understand the anti-doping rules and that their family, friends, coaches and athlete support personnel understand them too.
"They need to be aware of the risks their career faces if they test positive, and ensure they manage that risk at all times."
McMillan began his career at Rangers and had loan spells at Hamilton, Queen of the South and Wrexham before joining Dunfermline in January 2012.
He joined Partick Thistle the following March and was sacked by the Jags on 28 February this year following an investigation by the club.
Former Partick Thistle defender Jordan McMillan has been banned from all sport for two years by UK Anti-Doping (Ukad).