Football-Italia.net are reporting that the two clubs have agreed an initial €26 million fee for the Moroccan international.
Chelsea and Manchester United were strongly linked with a move for the defender over the summer but it appears that Bayern Munich have won the battle to secure the highly-rated defender.
Bayern Munich will pay a further €4 million in bonuses if targets are met.
It is understood that Benatia has agreed a five-year deal with the German Bundesliga champions, to receive €4 milli0n per season.
Mehdi Benatia is due to fly to Munich tomorrow to undergo his medical and complete the formalities on his transfer.
If these reports are accurate, Manchester United have now missed out on centre-backs Benatia, Thomas Vermaelen and Stefan de Vrij whom they were heavily linked with this summer.