The Real Madrid forward beat team-mate Gareth Bale and Atletico Madrid striker Antoine Griezmann in the voting.
Ronaldo, 31, scored the winning penalty for Real in the Champions League final against Atletico and captained Portugal to Euro 2016 glory in July.
Lyon and Norway striker Ada Hegerberg won the women's award.
She beat France's Amandine Henry and Germany's Dzsenifer Marozsan, after winning the Women's Champions League and a French league and cup double with Lyon.
Cristiano Ronaldo has been named Uefa's Best Player in Europe for the second time after winning the Champions League and Euro 2016 last season.