The award was handed to Netherlands captain at the end of the UEFA Champions League group stage draw ceremony, held in Monaco.
Van Dijk, 28, made his first appearance on the final three after helping Liverpool win the Champions League title last season. Ronaldo, a three-time winner, has been ever-present since the award was created in 2011.
"It's been a long road but that's part of my journey, it's part of who I am. I needed it like this, I'm not a player who was 18 years old and had that rise straight away. I had to work hard for every step of the way -- that's part of me and I'm very happy about that," Van Dijk said.
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Two-time award winner Messi was the leading scorer in both La Liga (36 goals) and the Champions League (12 goals) last season but his Barcelona side fell in the semifinal stage to Liverpool, who overcame a three-goal deficit in the second leg to advance.
Ronaldo and Messi, who have dominated the game's individual awards for the past decade, sat next to each other at the UEFA event and Ronaldo reflected on no longer being in direct competition with the Argentine in the Spanish league.
"It was a special year. I was curious because we've shared the stage here for 15 years. Of course, we have a good relationship. We have not yet had dinner together yet but I hope in the future," the Portuguese star said laughing.
Van Dijk was voted both the Premier League Player of the Season and the Players' Player of the Year, and was instrumental in Liverpool's sixth European Cup triumph.
The centre-back transformed Liverpool's defence since joining them from Southampton in January, 2018 for a then world record fee of £75 million for a defender with his physical presence and superb reading of the game.
Van Dijk began his career in his homeland with Groningen and moved to Scottish club Celtic before heading to the Premier League, where he helped Liverpool to runners-up spot last season as well as a Champions League triumph over Tottenham Hotspur.
He was also awarded the best defender award of the Champions League, with teammate Alisson Becker given the goalkeeper prize. Messi won forward of the year, and Barcelona's Frenkie de Jong took the midfielder award after leading Ajax to the Champions League semifinal round last season.
Manchester United legend Eric Cantona was one of the highlights of the event for his interesting speech after he was given the UEFA President's Award.
Information from Reuters was used in this report.