The Portuguese is adamant that his compatriot deserves the accolade because the 27-year-old forward played such an integral role in the club's title success
Messi broke record after record during a season in which he netted 50 times in La Liga but Mourinho believes that Ronaldo's 46 strikes carry more weight because they were crucial to Los Blancos' title success.
"Cristiano has to be the Ballon d'Or winner, not because he was the top scorer, which he already was last season, but because his goals won the league," the Portuguese said of his compatriot in an interview with SIC.
"Messi scored 50 goals that have not been worth anything, just as Cristiano scored 42 last season that were not worth anything.
"Cristiano has not been able to win the top scorer award and I think that should now be offset by the Ballon d'Or."
While Mourinho is in no doubt that Ronaldo is the best player in the game today, he does not believe the 27-year-old attacker is capable of inspiring his country to glory in this summer's European Championship.
"Real Madrid is one thing, and the national team another," the two-time Champions League winner argued. "Clubs, as usual, are better.
"With Portugal he does not have the support he has at Madrid and we cannot expect him to take us to the title and make 10 or 15 goals. And this, in spite of the fact that he is the best player in the world."
Turning his attention back to Madrid's Liga triumph, Mourinho claimed that finishing above Barcelona ranks as one of the greatest achievements of his stellar coaching career.
"I can honestly say that this has been the most difficult of the seven championships I have won as a coach - and I won one with Inter in the last game," he pointed out.
"This has been the most difficult because we had an opponent who is recognised as the best team of recent years.
"And as the games passed we came under enormous pressure because we could not afford to lose points. It was a titanic struggle between the two best teams in the world."
Mourinho added that winning the league with a record-breaking haul of points made the victory all the sweeter.
"The important thing was to win the title, but when we secured it and realised we could reach 100 points, we then had a high motivation to go in search of those victories," he explained.
"Real have won 32 league titles, but this team will be remembered for the 100 points, because at the moment that is unique and, I think, very difficult to overcome."