Iniesta, 26, scored the winning goal in Spain's World Cup final victory over the Netherlands in Johannesburg in July and, along with his 30-year-old midfield partner Xavi and Argentina forward Messi, helped Barcelona to the Spanish league title.
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Messi, 23, had a disappointing World Cup by his own high standards, failing to score in the tournament as Argentina, coached by Diego Maradona, crashed out after a 4-0 defeat by Germany in the quarter-finals.
"It's an honour to be one of the three finalists for the Ballon d'Or, and even more so to be there with Xavi and Leo," Iniesta wrote on his Facebook page.
"It's a marvellous prize for the cantera", he added, referring to the club's "La Masia" youth academy where all three trained.
Spain's Vicente del Bosque, a former Real Madrid manager who masterminded Spain's first World Cup success, made the shortlist for the Coach of the Year award.
He was joined by Barca's Pep Guardiola and Real Madrid's Jose Mourinho, who won the Champions League and Italian league and cup with Inter Milan last season.
FIFA general secretary Jerome Valcke told a media conference that Spanish soccer had been "really ahead of the rest" since 2008 and was also dominating at club level.
"They are crushing world football at the moment," he said. "Barcelona's match against Madrid last week was a brilliant display of football."
HISTORIC DAY
Guardiola, also a product of the "Masia" academy, said the "tremendous success" of Iniesta and Xavi should be shared with Del Bosque and his predecessor as Spain coach Luis Aragones, who led Spain to victory at Euro 2008.
"I am also happy for Leo, who is the greatest, although he did not have much luck at the World Cup," the former midfielder told a news conference before the club's Champions League Group D match at home to Rubin Kazan on Tuesday.
"The most important thing is that the one that wins shares it with his team mates.
"It will be an historic day and I want everyone who works at this club to feel it is theirs."
It was the third time that three players from the same team had been named on the three-man Ballon d'Or shortlist. In 1988 and 1989, AC Milan monopolised the first three spots, with Dutch striker Marco Van Basten winning both times.
This year's winners will be announced on January 10 in Zurich.
The honour was formerly organised solely by France Football magazine but has now merged with FIFA's World Player of the Year award. Messi won both in 2009.
