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 had been courted by a host of clubs, including the Bavarians and Manchester City, throughout the summer, but the Basque club were adamant that they were not going to let the player leave for less than his release fee.
Bayern themselves were initially hesitant to meet that price, but after confirming that they would be willing to do so a fortnight ago, they have finally got their man.
And the Spain international has spoken of his desire to help die Roten re-establish themselves after a barren season last time out.
"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 the wait is over.
"Playing here was my dream. Bayern are one of the best clubs in Europe and in the world, and I hope to win titles with them."
Meanwhile, Bayern director Karl-Heinz Rummenigge revealed that the Basque midfielder has taken a pay cut in order to push the deal through.
"Of course this is a large sum of money," he told FCB News. "But the player is indirectly participating in it by giving up a large sum of money.
"It was very complicated because we didn't have the co-operation of Athletic from day one. 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."
The midfielder, who can also play at the heart of defence, has signed a contract that expires in June 2017. He had spent six years at San Mames after joining from Osasuna for €6m at the age of 17.