Mario Gomez' double in the first half put Germany in complete control of the Group B encounter.
Rafa came on for the second half and played in a deeper midfield role as Holland tried to claw their way back into the game.
Robin van Persie pulled a goal back in the 73rd minute and Rafa had a decent strike wide from distance but Germany were comfortable enough for their 2-1 win.
The result means that Holland have to beat Portugal in their final group game, hope Germany beat Denmark and then have a better goal difference than both Denmark and Portugal to progress on three points.
Spurs interest today will see Luka Modric and Vedran Corluka back in action as Croatia take on Italy in Group C, kicking-off at 5pm in Poznan.
Croatia began the tournament with a 3-1 win against the Republic of Ireland on Sunday and top the group after Spain drew with Italy in their opener.
Spain take on the Republic in today's second match, kicking-off at 7.45pm in Gdansk.