The 24-year-old finished ahead of Olympique Lyonnais midfielder Miralem Pjanic, Montpellier defender Emir Spahic and Galatasaray playmaker Zvjezdan Misimovic.
"Receiving an award like this, especially for a second time, brings not only great honour but also responsibility," said Dzeko.
"The list of nominees was again strong, and if any one of my international team-mates had received this award instead of me, it would have been well deserved.
"I expect a difficult year ahead of me both at Wolfsburg and with the national team, where we are aiming to reach Euro 2012."
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