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.”
Klopp’s men are likely to be in contention for individual awards again next year should they finally end a 30-year wait to win a league title.
Liverpool lead the Premier League by eight points and host local rivals Everton in the 234th Merseyside derby looking to inflict more pain on the blue half of the city.
Everton are just two points above the relegation zone in 17th, but Klopp insists the clash between the two remains the “standout” fixture of the season for Liverpool.
“This is the standout game for both teams during the season and both teams always showed that and respected that. We have to make sure that we are ready,” added the German.
Marco Silva’s position at Goodison Park is under huge threat but the Portuguese has been given the chance to turn his time at Everton around by recording a first victory over Liverpool at Anfield since 1999.
“They want to strike back, they want to show that they can do different. They can sort a lot of problems in one game,” said Klopp.
“When you are connected to this club then this is a game –- whichever situation you are in –- you want to win and that’s what we have to show.”
Silva earned plaudits for a change of system and upturn in performance for Sunday’s trip to second-placed Leicester, which only ended in a 2-1 defeat thanks to Kelechi Iheanacho’s stoppage-time winner for the Foxes.
And he is hoping a historic upset could transform Everton’s season.
“It would have a very good impact, no doubt about it. It will not wipe out anything we did in the last one-and-a-half, two months, but it will be very important for us,” said Silva.
“It can give us the chance to get points which we need and for sure it can give confidence to our players.”