It was the most highly anticipated rematch in UFC history, given that Sonnen is the only man in UFC history to come close to beating Silva and also due to the tremendous job Sonnen did in hyping the fight.
In the first round, it looked like the champion was in trouble. Sonnen managed to take him down with ease and control the whole round from the top position, even mounting Silva at one point. In the second, Silva managed to stuff several takedown attempts and rock Sonnen standing. Eventually Sonnen dropped and the champion followed up with punches to end the fight.
Without a doubt, it was the biggest win of Silva's career, but the performance left some fans with a bad taste in their mouths.
A few reasons.
First, before the fight began, Silva took Vaseline from his face and wiped it on his body. The referee saw him do it and wiped him down as a result.
Then in the second round, Silva was warned about holding the shorts while clinching with Sonnen. A few moments later, as Sonnen attempted to disengage from the clinch, it was revealed that Silva was blatantly holding Sonnen's shorts and preventing him from moving away. During that time, Silva landed a couple big punches.
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After that, Silva had Sonnen down and against the cage and he threw a knee—the legality of which is still being hotly debated. If you follow the provided link, it looks like the knee hits the body, but also catches a bit of Sonnen's jaw (via Jacob Schmidt, Twitter).
That's three infractions—one of them debatable—inside of two rounds. With all those facts in order, it's difficult to say that Silva's victory isn't at least slightly controversial.
Silva was likely en route to victory either way. In the second round he was stuffing all of Sonnen's takedowns and that means it was just a matter of time. It's just unfortunate that it wasn't a completely clean victory.
Similar to Jose Aldo's title fight with Chad Mendes, in which Aldo knocked Mendes out shortly after holding the cage to prevent a takedown, people will always be left to wonder if Silva would have won, had he fought a totally clean fight.