PSG's ultra supporters have not forgiven Messi or his teammates for that debacle and walked out of the stadium early as a sign of protest instead of staying and celebrating the league title following their 1-1 home draw with Lens.
"To judge Messi in this way is unfair," Pochettino said.
"You can't talk about Messi that way. It is like when I talk about Maradona. I'm not talking about an ordinary player. Messi is on the same level as Diego Maradona.
"I have no doubts about his quality. Messi has enough talent to do what he has to do. He will do it. Next season will be completely different for him. It was a year of learning, and not just on a professional level coming to Paris Saint-Germain, in a new league and with new teammates, but also on a family level. You must take that into account. It is a significant upheaval that can affect a player."
Messi, 34, only scored nine goals and set up 13 in 31 appearances across all competitions after joining PSG as a free agent in August following his 20-year career at Barcelona.
In his last season with the Catalan giants, Messi had a total of 38 goals and 14 assists in 47 appearances.
The Argentina captain has one year left on his contract with PSG.
"It is clear that the move from Barcelona to Paris Saint-Germain was a change in which a process of adaptation was necessary," Pochettino added.
"Certain circumstances did not allow him to feel as comfortable as in Barcelona, where he had spent 20 years, where he had been the flagship player."