Gareth Bale walked away with the honour on a night of personal glory at a plush London ceremony on Sunday night.
That Nastasic did not even make the six-man nominations list left Lescott stunned, particularly as the 20-year-old Serb is responsible for him spending so much time on the sidelines this season.
"I have no gripe with him. You don't begrudge someone who comes in and does well," said Lescott.
"It was a bit harsh he was not nominated for PFA Young Player of the Year.
"He plays beyond his years and if he was English he would have had a lot more recognition.
"He's not a glamorous sort of player who comes out with the ball. He just does his job exceptionally well."