The Spaniard was cleared to take part in Sunday's warm-up but felt unwell and withdrew from the race with low blood pressure, race organisers said on the MotoGP website (www.motogp.com).
"After a medical check-up on Sunday morning, he was cleared to take part in the warm-up but ultimately did not do so due to feeling unwell," said a statement
"Further checks resulted in a decision from Repsol Honda Team and Pedrosa himself to withdraw from the race due to low blood pressure.
"He will be examined upon his return to Barcelona on Monday, before discovering early in the week whether or not it will be possible to race at Laguna Seca (in the U.S.) next weekend."
World champion Jorge Lorenzo, Pedrosa's nearest challenger, will also miss the race at the Sachsenring. He withdrew on Friday after crashing in practice.