"I see it slightly different, I think it's normal and a lot of people see it slightly differently."
Klopp said Messi was probably the best player he had seen in his lifetime and deserved to be a six-times winner.
"But the last season, if you really go for only that season, then I cannot remember a more impressive season for a defender ever, honestly," said the German.
"So it would have been right as well if Virgil would have won it."
Italian Fabio Cannavaro was the last defender to win the Ballon d'Or, in 2006, after helping Italy in the World Cup.
The award has been dominated by forwards, with Portugal's Cristiano Ronaldo a five-times winner and third on Monday.
Van Dijk transformed Liverpool's defence on the way to winning last season's Champions League and helped the Netherlands reach the Nations League final in Portugal.
He became in August the first defender to win UEFA's Men's Player of the Year and was runner-up in September, to Messi again, in the FIFA Men's Player award.
Wednesday will revive good memories for the 28-year-old, who scored the winner on his debut in the Merseyside derby last year after joining from Southampton in a reported world record fee for a defender.
While Liverpool are eight points clear of Leicester City at the top of the standings, Everton are just above the drop zone in 17th and the pressure is on their manager Marco Silva.
"I have sympathy for him," Klopp said. "I know how hard being a manager can be. But I think the last thing Marco needs right now is for me to feel sorry for him. I’m really on his side because I know about the job."
Everton will also play Liverpool in the third round of the FA Cup in January. (Reporting by Alan Baldwin, editing by Ed Osmond)