Craig Stillwell and Carla Andrews's baby girl Effie was taken away from them for almost eight months.
It has emerged she has a rare medical condition, known as Ehlers-Danlos syndrome type IV (EDS), which causes "easy bruising".
The case has been stopped and Effie is home with her parents in Aylesbury.
Mr Stillwell was arrested at Stoke Mandeville Hospital, accused of causing grievous bodily harm after Effie collapsed last August, aged five months.
"The hospital treated us like monsters," he said.
"It was heartbreaking."
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Effie was put in foster care and her parents were permitted to see her just three times a week for 90 minutes at a contact centre.
Buckinghamshire County Council took the case to the family court, seeking to put the little girl into local authority care.
Miss Andrews researched what could have caused bleeding on her daughter's brain and tests revealed she suffered from EDS IV.
The condition is characterised by "thin and translucent skin, easy bruising, vascular and arterial rupture".
The council's application was withdrawn last week and the judge Karen Venables said the family had experienced "unimaginable horror".
Miss Andrews said it was "amazing" to have her daughter back home.
The couple, both 23, said they were not going to take any action against the authorities but wanted to raised awareness of the condition.
Miss Andrews said: "I feel bitter towards the hospital. I know they have to do their job but they should've gone about it differently."
Mr Stillwell added: "We want to get the awareness out there that these connected tissue disorders do exist.
"They may be invisible but they can cause a lot of damage and they do mimic child abuse and shaken baby syndromes."
A couple accused of hurting their daughter in a suspected shaken baby case said they had been treated like "monsters".