The Holland captain came second to the Argentina forward despite having a huge influence on the Reds winning the Champions League and overcoming Messi’s Barcelona in the semi-final.
“I see it slightly different and a lot of people see it slightly different but that’s absolutely no problem,” said the Liverpool manager.
“Lionel Messi, I’ve said probably 500,000 times in my life already, is probably the best player I saw in my lifetime.
“But I cannot remember a more impressive season from a defender ever. Honestly. So it would have been right if Virgil won it, I heard it was pretty close.”
On Wednesday Liverpool host Everton in the 234th Merseyside derby, with the relegation-threatened Toffees looking to break a winless streak on the ground dating back to 1999.
It has left manager Marco Silva’s position under huge threat but while Klopp had sympathy for his counterpart he did not feel sorry for the Portuguese.
“Of course I have sympathy because I know how difficult the life of a manager can be,” he added.
“But the last thing Marco needs now is that I feel sorry for him – I don’t. But I am really on his side because I know about the job.”
Speaking about Wednesday night’s Anfield clash, Klopp said: “Sometimes a win can give you a boost, but in this game (last season) Gomez saved one on the line, Everton were good and intense. The final moment was a strange goal. My celebration, I said sorry for. Won’t happen again, not even in a derby. It has nothing to do with Wednesday.
“We are in a better moment, that us obvious. But if it is a derby we would love to win. Everton want to strike back and they can do it differently, They can sort problems with a win. There is no doubt about this team.”