It is the Barcelona midfielder's second major individual honour of the summer, after he was named Player of the Tournament for his role in Spain's triumph at Euro 2012 in Poland and Ukraine.
The award was decided by 53 European journalists who cast their votes during Thursday's Champions League group-stage draw in Monaco.
Iniesta (28) received 19 votes, with Ronaldo and Messi – the winner of last year's inaugural prize – each receiving 17.
"I am very honoured and I dedicate this award to my Barcelona and Spain teammates," said Iniesta, who received the award from Uefa president Michel Platini.
"I am privileged to be here with two such great footballers as Leo and Cristiano."
An artful attacking midfielder, Iniesta has won every major honour in the game with Barcelona and Spain over the last four years and notably scored the extra-time winner against the Netherlands in the 2010 World Cup final in South Africa.
Despite his success at Euro 2012, Iniesta saw Barcelona miss out to Ronaldo's Real Madrid in last season's La Liga title race, while the Blaugrana also fell to eventual champions Chelsea in the semifinals of the Champions League. – AFP