The Argentina captain won the Golden Ball award, given to the best player of the tournament, but has come under criticism from all corners with many, including Diego Maradona insisting he didn't deserve the award.
But Mourinho has leapt to his defence, insisting that he doesn't need to win the World Cup to be identified as one of the best players of all time.
"It's easy to respect him when he has won but when he has lost, it's not so easy," the Chelsea boss told Yahoo.
"He is still a historical player. He does not need to be world champion to be a historical player, especially in this last decade.
"For me Pele is Pele and Maradona is Maradona. It's not for me to compare players from different generations.
"Maybe because he is from the same generation as when I was born - for me Maradona is Maradona."
When asked if he felt Messi was a scapegoat for Argentina's failings, Mourinho replied: "Not at all," before going on to question Albiceleste coach Alejandro Sabella's decisions in the final defeat to Germany.
"I think in the first half he had fantastic options," he added. "I would like to know why Lavezzi stayed in the dressing room at half-time.
"Argentina had been playing with two lines of four, with Enzo Perez closing Phillipp Lahm and Lavezzi doing the same on the other side. Because they were so compact Messi could walk while defending and then when he got the ball he had the energy to make the difference.
"When Sabella brought Aguero on for Lavezzi, Argentina changed from a 4-4-2 to a 4-3-3 and they lost a lot of balance. Messi had to run much more after Lavezzi went off.
"The team lost balance and especially energy - energy that they needed in extra-time."