The Dutch captain came second to the Argentina forward despite playing a huge role as Liverpool won the Champions League last season, 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 Klopp.
“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 Virg won it. I heard it was pretty close.”
On Wednesday, runaway Premier League leaders 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.
Marco Silva’s position is under huge threat but while Klopp had sympathy for his counterpart he said 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 told his pre-match press conference on Tuesday.
“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.”