Kazakh Golovkin, 37, was fighting for just the second time since losing to Saul Alvarez in Las Vegas in September 2018.
He knocked down the Ukrainian in round one and cut him in round two but the rest of the fight became a slog.
Judges awarded the fight to Golovkin 114-113, 115-112, 115-112.
“After the first round I didn’t think this was an easy fight. I told myself this is a tough fight,” he said.
Golovkin was stripped of the ibf title last year for refusing to make a mandatory defence against Derevyanchenko, 33. He opted instead for a rematch with Alvarez – which ended with Golovkin suffering the first defeat of his career.
Golovkin and Alvarez had drawn a lucrative first encounter.
The nature of Canelo’s win in that second fight – by a close majority decision – and the fact their two battles are among the biggest-grossing fights in history, has meant the prospect of Canelo v Golovkin Three has often been talked about.
And when asked about that in the ring after Saturday’s fight Golovkin said: “Right now I know exactly what I need. I understand I need more,” he said.
“Everything is ready. Just call to Canelo and if he says yes, let’s do it.”