The 23-year-old has signed a five-year contract with the Bavarian side after the German champions were finally able to resolve legal and tax issues
The 23-year-old has been courted by a host of clubs, including the Bavarians and Manchester City throughout the summer, but the Basque club was adamant that it was not going to let the player leave for less than his release fee.
Bayern itself was initially hesitant to meet that price, but after confirming that it would be willing to do so a fortnight ago, it has finally got its man.
"Of course this is a large sum of money," club director Karl-Heinz Rummenigge told FCB News. "But the player is indirectly participating in it by giving up a large sum of money.
"It was very complicated. We are very happy that Javi Martinez is finally with us. In recent days, we still needed to resolve tax and legal problems. Fortunately for us, we've succeeded."
For his part, the Spain international has spoken of his delight at finally securing a move to the club after such a potracted saga.
"I am very happy and I'm looking forward to playing for a club with such a history," he told FCB.tv. "I've had a very long wait, but finally thei weight is over."
The midfielder, who can also play at the heart of defense, has signed a contract that expires in June 2017. He has spent six years at San Mames after moving to the club from Osasuna.