Hernandez, who will link up with France teammate Benjamin Pavard at Bayern following his transfer from VfB Stuttgart, joined Atlético at the age of 11 but admitted he was delighted to make the move after months of negotiation.
Bayern also are in need of reinforcements out wide, with Franck Ribéry and Arjen Robben to leave at the end of the season.
The Bavarians have identified Lille standout Nicolas Pépé as their prime summer transfer target. The Ivory Coast international has been in particularly impressive form this season.
They have already reportedly met with Pépé’s representatives, with the player also keen on a move to the Allianz Arena.