Manquillo was forced from the field in the 44th minute following a collision with Cristiano Ronaldo in the semi-final of the the Copa del Rey as Diego Simeone's side lost 2-0 in the second leg and 5-0 on aggregate.
The 19-year-old was thrown completely off balance and fell awkwardly, landing on his face and placing considerable pressure on his neck.
And the club confirmed in a statement on Wednesday that the teenager had been diagnosed with whiplash.
"The posterior part of the medical tests that he underwent confirm that Javier Manquillo suffers whiplash with normal radiologic tests," the statement said.
"A neurological examination came out normal and is admitted for observations."
Ronaldo was in the thick of the action as he scored two penalties and was hit by an object - thought to be a lighter - thrown from the crowd.
