McMillan tested positive for benzoylecgonine, a metabolite of cocaine, following Thistle’s game against Celtic on 3 December last year.
The 26-year-old was suspended by the club and sacked following an internal investigation.
UKAD confirmed that McMillan was handed a two-year ban in April and that decision has been upheld following an appeal from the player.
The former Rangers and Dunfermline Athletic player has vowed to continue fighting to clear his name after claiming his drink was spiked. He will not be able to play football until 17 December, 2016.
UKAD chief executive Nicole Sapstead said: “UKAD’s role is to protect the integrity and spirit of sport, and athletes, at all levels, need to understand the importance of strict liability – 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.”
McMillan was quoted as saying: “It’s so easy for your drink to become contaminated without your knowledge.”