In the first round, Palhares abruptly stopped punching a downed Miller and began celebrating.
Referee Herb Dean never indicated that the fight was over and would instruct both participants to resume fighting. After three rounds, Palhares walked away with a unanimous decision.
Despite an impressive performance, Palhares' first-round celebration left many onlookers questioning what prompted his behavior. Palhares' trainer Murilo Bustamante would explain his fighter's action Sunday via Twitter.
"Just to clarify what happened during Toquinho's fight. He told me that he stopped because his opponent said 'stop, stop, stop' when he was punching him hard," he tweeted.
"Then he stopped (hitting) him and thought that the fight was over and went to celebrate. Who can say now that 'Toko' isn't a fair fighter? He is just too naive, but he has a big heart."
Miller strongly denied ever uttering the word "stop" at any point in during the fight.
"I absolutely did not say, 'stop, stop, stop!'" Miller told ESPN.com. "Absolutely not, and I mean that one-thousand percent!"
Dean said that at no time did he call the fight off. The highly-respected referee added that had he opted to stop the fight off he would have done much more than waive his hands.
"I'm not saying that Dan didn't say stop, but I didn't hear him say that," Dean told ESPN.com. "I can't say what Rousimar heard or what Rousimar did not hear. But I did not hear Dan say anything.
"If I'm going to stop a fight, I usually always touch the fighters. Even if I'm waving a fight off, I'm going to be touching you with some part of my body.
"I might be pushing him off with my legs and chest, while waving the fight off. Somehow, I am going to touch them. I wasn't ready to stop the fight."
Miller's trainer Mike Constantino said he respects Palhares, but that the Brazilian simply made a mistake inside the Octagon. Constantino points to several factors why Palhares' claim should be dismissed.
"I find it hard to believe," Constantino told ESPN.com. "With the roar of the crowd, the fact that (Palhares) doesn't speak English, and the fact that he is known to hold submissions extra long, there is no way that he's going to show mercy on Dan in his home country and just pull up because he assumes that (Dan) said 'stop, stop, stop.' And the referee never pulled him off."
Franklin McNeil covers mixed martial arts and boxing for ESPN.com. Follow him on Twitter at www.twitter.com/Franklin_McNeil.