The 32-year-old beat Madrid team-mate Pepe and Sporting CP goalkeeper Rui Patricio to the prestigious individual award at the Quinas de Ouro gala on Monday.
Ronaldo led Madrid to Champions League glory as they beat Atletico Madrid in the final, with the forward netting the decisive spot-kick in the shootout in Milan after scoring 16 times en route to the decider to become the competition's top scorer.
He went on to help Portugal to their first major trophy at Euro 2016, seeing off hosts France 1-0 after extra-time in the final in Paris, despite Ronaldo being forced off in the first half through injury.
"It was a very special year for me because the Euros was the only trophy I was still missing," Ronaldo said.
"I want to thank the Portuguese people again, they gave us confidence on our way to the title."
The prolific attacker previously won the Ballon d'Or and FIFA's The Best award to cap a sublime 2016.
Bayern Munich youngster Renato Sanches was voted young player of the year, while national team coach Fernando Santos lifted the coach of the year award.