Ronaldo was pivotal in Real Madrid's La Liga title success last season, but Iniesta, who endured a trophiless season with Barcelona, was voted as the most impressive performer in Europe.
Mourinho told CNN: "Iniesta is a superb player. There is no doubt about that. However, he did not have such a great season.
"He was great at Euro 2012. He won the Euro's but we should not forget that this is a competition that lasts only three weeks.
"I think Cristiano had good reason to be upset with UEFA's decision."
Barcelona host Real Madrid in the El Clasico derby on Sunday.