The Liverpool defender took the honour ahead of Barcelona captain Lionel Messi and Juventus superstar Cristiano Ronaldo.
Van Dijk's arrival from Southampton made him the world's most expensive defender and he helped repay his fee by starring as the Reds won Champions League glory last term.
"I need to thank all my team-mates and the staff. I wouldn't have achieved what I have over the last year [without them], my family of course, it's been a long road but it's part of my journey, who I am," Van Dijk said.
"I had to work hard every step of the way, it's part of me and I'm happy about that. I'm proud to get that trophy and it's a credit to everyone who helped me along the way.
The Netherlands international is considered a leading contender to win this year's Ballon d'Or, which has not been given to a defender since Italy captain Fabio Cannavaro triumphed in 2006 having led the Azzurri to World Cup glory.
Taking the Women's Player of the Year award was England right-back Lucy Bronze, who beat out Lyon team-mates Ada Hegerberg and Amandine Henry.
UEFA also handed out positional awards for male players, with Van Dijk landing Champions League Defender of the Season recognition in addition to taking the top prize.
Midfielder of the Season went to Frenkie de Jong for his performances in Ajax's stunning run to the semi-finals, while Forward of the Season was given to Messi.