The Sweden captain has enjoyed a stunning tenure since moving to France in the summer of 2012 - scoring 35 goals and assisting 11 times last season as the club claimed the Ligue 1 title - while he has already netted 11 times and set up five goals so far this term.
Despite his fantastic run, Motta has tipped one of the La Liga duo to come away with the prize.
"To win the trophy itself will be difficult," Motta said in a press conference.
"There are still two top players, Messi and Cristiano Ronaldo. They've demonstrated a higher level, Messi perhaps even more than Ronaldo."
The 23 nominees for the Ballon d'Or were announced on Tuesday.