The unbeaten Kazakhstani put Ishida out with a fierce straight right after putting the Japanese challenger under heavy pressure for the first two rounds.
The win marked his seventh successful title defence and when asked who was next, the 26-0 Golovkin simply said: “It doesn’t matter.”
The card saw Edwin Rodriguez win a battle between undefeated boxers as he earned a super-middleweight success over Ezequiel Maderna over 10 rounds.
The contest, which Rodriguez won with scorecards of 96-92, 96-92 and 95-92, was one of two semi-finals in the ‘Million Dollar Super Four’
He will fight Denis Grachev in the final after Grachev inflicted a first defeat on former world champion Zsolt Erdei via split decision (96-94, 96-94, 94-96).
On the same card Sergey Rabchenko retained his European light-middleweight strap with a business-like stoppage of Italy’s Adriano Nicchi in three rounds.
The Belorussian is a protégé of former world champion Ricky Hatton, and relocated to Britain in 2011 to train under the tutelage of ‘The Hitman’.