Reigning WBA, WBC and IBF champion Golovkin put his titles on the line during the fight in Las Vegas, but the judges could not separate the two men after 12 gruelling rounds.
Mexican Alvarez appeared to enjoy the better of the early rounds and also ended the fight strongly, but Golovkin dominated the middle exchanges and landed more punches.
Judge Adalaide Byrd made Alavarez the clear winner, while Dave Moretti scored the bout in Golovkin's favour and Dan Trella could not separate the two, resulting in a draw, despite the crowd at the T-Mobile Arena clearly believing the victory should have gone the Kazakh fighter's way.
Golovkin, who remains unbeaten in 38 professional fights, also felt he should have been awarded the victory after revealing his views on social media.
He tweeted: "The world knows. Thanks to all my fans from all over the world for your support. It means a lot for me."
Alvarez, much to the disbelief of the majority of the crowd, felt he had the better of the fight, but his record now stands at 49 wins (34 KO), two draws and one defeat from 52 fights.
A rematch between the two is now expected to take place after both fighters confirmed their desire to lock horns once again.