Alcantara has long been expected to join Premier League champions Manchester United, but has now instead joined the Champions League winners.
The youngster will link up with former Barcelona boss Pep Guardiola at Bayern Munich.
Bayern Munich have agreed to pay a fee of 25 million euros for the Spain Under-21 midfielder.
Thiago will have a medical in Munich in the next few days before signing a four-year contract with Bayern, the club confirmed on their website.
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Summer 2016 is set to be a very exciting time for football fans, as this is when the long awaited Euro 2016 tournament kicks off.
Since Guus Hiddink arrived at the helm, Chelsea have improved considerably after a tricky start to the campaign.