But judges Dave Moretti and Steve Weisfeld each saw it 115-113 for Alvarez, giving him the win and handing Golovkin his first defeat.
Alvarez looked close to tears after a decision which will again prompt controversy as, for spells in the fight, Golovkin seemed to be edging the physical side of a tactical battle, with his jab proving key early on. After 12 rounds, Alvarez would be announced the victor of the bout via majority decision, winning the WBC middleweight title.
The championship rounds was drama with the fight close Golovkin took it to Canelo landing big punches but Alvarez responded with punches going after the champ.
WBN scored it 115-113 in favor of Golovkin, although all three judges agreed with eight rounds on every cards (including the WBN card).
A year after the two fought to a draw, the second fight was nearly as close.
Golovkin beat Vanes Martirosyan as a replacement opponent on May 5 at T-Mobile Arena.More news: It's not just FEMA: ICE quietly got an extra $200 million
Victory was sweet for Alvarez, who had been accused of "running" during last year's first encounter by Golovkin's camp.
Golovkin endured a slow start - by his standards, before taking over the contest in the mid-to-late rounds and seemingly doing enough - but only just.
There was plenty of enthusiasm heading into last September's fight between Canelo and GGG, which included some memorable moments and flurry of punches. This time it was Golovkin who was upset, and he stormed out of the ring without talking.
Later, Golovkin told reporters: "I'm not going to say who won tonight, because the victory belongs to Canelo according to the judges". He's a very good fighter.
"I think he's scared".
Ringside punch stats showed a close fight, though they favored Golovkin by a small margin. Instead Alvarez slow-played negotiations, faced Golovkin when he was ready, scoring a draw and now a majority decision - the only two blemishes on Golovkin's record (38-1-1). Great fight with two great champions!' I promised the people I would go for a knockout. (When asked about a third fight) Under the right conditions, yes.