The United Soccer League championship said in a statement that Flemmings had been found guilty of using "foul and abusive language in the form of a homophobic slur" during Phoenix's game with San Diego Loyal on September 30.
San Diego's players walked off the pitch in protest following the incident, with Loyal coach Landon Donovan later backing the decision.
Jamaican international Flemmings had strongly denied abusing San Diego's Collin Martin, who is openly gay.
"At no point did I say a homophobic slur towards Collin Martin," Flemmings said after the incident. "I do not know Collin personally, but I respect all my opponents equally, Collin included.
"I am disappointed by San Diego's actions ... I have been mauled and ridiculed online with no opportunity to defend myself."
The USL however said it had reached its decision against Flemmings after interviews with 11 individuals including players, coaches, and match officials.
In a statement on Tuesday, Phoenix Rising manager Bobby Dulle said the club had accepted the investigation's findings, and noted that Flemmings would spend the remainder of his contract, which expires next month, on administrative leave.
"Phoenix Rising accepts and supports the results of this investigation," Dulle said. "These actions could not be more contrary to the core values of our organization, and we apologize to all who were affected."
The club said Flemmings, whose contract concludes on November 30, would be provided with "resources he needs to learn and grow from this, so that he may become a model for change in our sport."
"We will use this as an opportunity to learn, grow and be a force for change, as we work towards eradicating bias from our sport and our community," Dulle added.
San Diego's decision to abandon last week's fixture effectively ended the team's chances of reaching the USL's post-season playoffs.
However coach Donovan, former star of the US international team, said the players had no doubt about their decision.
"Our guys, to their immense credit, just said, 'We're not going to stand for this,'" Donovan said.Â
"They were very clear in that moment that they were giving up all hopes of making the playoffs, even though they were beating one of the best teams in the league handily.
"But they said that doesn't matter, there's things more important in life and we have to stick up for what we believe in. And so they made the decision to walk off."
Standout matches today