The Real Madrid star sustained a nasty eye injury early in the Spanish champions' 2-1 win at Levante and was ruled unfit by Portugal national team doctors.
Ronaldo was caught in the face by defender David Navarro but soldiered on, even giving Madrid the lead before being substituted at half-time.
Madrid boss Jose Mourinho"He's dizzy. In the first half he was unable to see properly with that eye, but during the break he couldn't see properly with either. So it was impossible for him to continue," said .
"When he gets to Madrid he'll go to hospital to have the tests he needs."
Valencia defender Joao Pereira and Dynamo Kiev midfielder Miguel Veloso have also pulled out of the clash in Libreville.
Portugal coach Paulo Bento has called up Maritimo's Ruben Ferreira and Hugo Viana of Braga as replacements.