The Blaugrana star posted a treble against the Boquerones to take his tally for the season to 68, thus surpassing Gerd Muller's record for most goals in a single European campaign
The Argentina international netted three times in a 4-1 win for the Blaugrana to take his Liga tally for the season to 46 goals in 36 games, moving him two clear of Cristiano Ronaldo in the battle for the Pichichi.
There are those that believe that the latter is just as talented as the Rosario native, but Pellegrini believes that Messi is in a class of his own.
"I don't know the parameters for the Ballon d'Or," the Argentine coach mused. "I only know that Messi deserves to win every trophy."
Pellegrini was also full of praise for outgoing Barca boss Pep Guardiola, who announced last week that he will be standing down at the end of the season.
"Guardiola's contribution to football has been immense, not only for the titles he has won, but for the game he has implemented and the quality he has shown as a person," the former Real Madrid coach said.
"Pep has made the best decision for him, but I think he will only take a short break. Certainly, people will be hoping that he only takes a little time off as the game needs him."
Turning his thoughts back to the game, Pellegrini insisted that he was far from downbeat after his side's defeat in Catalunya, arguing that the final scoreline flattered Barca.
"We did not lack ambition and the result did not reflect what happened at all," he stated. "We played a good game and did not deserve to lose.
"[Barcelona goalkeeper Jose] Pinto made three very important saves and Messi's two penalties decided the game.
"But we just have to keep fighting in these last two games to finish as high up the table as possible because I think that Malaga has had a very good campaign.
"We were fighting for the relegation last season and now we are fighting for a place in Europe."
In spite of their loss, Malaga remain fourth in the standings, three points above fifth-placed Levante.