Two judges scored it 115-113 for Alvarez, with the third judge scoring it 114-114.
Judge Glenn Feldman had it 114-114, the same as Yahoo Sports.
The two fighters switched roles from their first fight, with Triple G trying to counter Alvarez and the Mexican fighter coming forward much of the fight.
After another 12 rounds of fighting against "GGG" the judges declared Canelo the victor via Majority Decision.
"I showed my victory with facts", Alvarez said in his postfight interview.
The match was among the most anticipated, if not the most anticipated, fights of the year after their initial encounter ended up rather unconvincingly.
Note: Golovkin has taken 8-stitches, the cut was 5 cm. long on his right eye.
"I'm very excited, very emotional".
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Alvarez (50-1-2, 34 KOs), who is now the WBA, WBC and IBO middleweight champion, dealt Golovkin his first loss after going undefeated in his last 39 fights, including a split draw against Alvarez in their first bout previous year.
Boxing can be a fickle game in terms of how a fighter is perceived by the mainstream majority where you're only as good as your last fight. And it came at the hands of the red-headed Alvarez, a Mexican star whose positive test for clenbuterol forced the rematch to be postponed from May.
"Because, even though he's a power-punching machine, he's also a very clever and intelligent fighter". (When asked about a third fight) Under the right conditions, yes.
If the people want another round, I'll do it again.
Sanchez, meanwhile, brushed off suggestions that Golovkin had once more been on the wrong end of a dubious performance by the three ringside judges.
In what was a tightly contested bout throughout the night, many observers were split as to who would be leading this one, but the large consensus was that GGG outboxed Canelo, who was on the verge of getting knocked out at certain stages. A GGG victory, like I had it, or 2.
Golovkin offered back huge shots of his own that at times looked to stop the younger man in his tracks, but the champion looked exhausted from the punishment to his midriff, if not a little shopworn and unable to withstand such onslaughts with the resilience he showed in the previous fight.
Many argued the two-weight world title holder "robbed" Golovkin of another victory.