Englishman Cooper has had a falling out with the club over several issues, including player movements, informing the team’s hierarchy of his decision several days ago.
Cooper today confirmed to The World Game that Saturday’s match at Kardinia Park in Geelong will be his last in charge of the side which finished second in the Thai Premier League last year.
"The club has high expectations and so do I," Cooper said. "It was a question of whether or not that ambition was being matched and in the end I decided it's better to part ways and this playoff will be my last match with the club."
Muangthong announced it has agreed to loan out its leading attacker, Thai international Teerasil Dangda, to Spanish club Almeria in June. It is understood the coach was less than pleased the club hadn't fully backed him in the transfer market.
It's believed the Muangthong players are yet to be informed of the development although Cooper expects his decision won't adversely affect the squad.
"They are all professionals and they have their pride on the line too so I expect we'll do all we can to trouble Melbourne," he said.
The squad has been dealt a further blow with news that its North Korean defender, Ri Kwang-chon, has been denied a visa to enter Australia.
"He's still in Thailand waiting to get his visa – our application was rejected and I was informed that it was done for political reasons," Cooper said.
A spokesperson from Football Federation Australia (FFA) strongly refuted that claim.
"We sent the club a letter of invite to Australia, as is our duty for all clubs visiting the country, on 2 January, informing them of the visa application process, which needed to be completed and submitted four weeks out from their trip," he said.
"They only applied one day before leaving. We worked with the Government and Department of Foreign Affairs to try and expedite the process for the club, and managed to get 27 of the 28 applications approved.
"The fact that one wasn't, is really only owed to the fact that Muangthong did not follow the rules."
It's understood that should Muangthong lose to Victory, it believes it will have firm grounds to appeal that result given the potential loss of Ri.
"It's my understanding that FIFA has rules around these sorts of matters and it's left a huge hole for me to fill," Cooper said.
"We had other foreign players we couldn't register to include Ri and now to hear this news is a massive blow."