The Brazilian midfielder joined Hanover in January and is likely to have already been infected with the virus when he travelled from his homeland, said Hannover.
"We are very sorry for Franca but the most important thing is that he recovers and returns healthy," sports director Joerg Schmadtke said.
"After treatment he will continue his career as a footballer according to the doctors. That is important and good news for him and us."
Club officials said it was "unlikely" for other players to have the virus but there will be blood tests conducted in the coming weeks.
The 21-year-old, who was far shorter than the 1.9 metres tall man the German team had been expecting when he arrived in January, signed a deal to 2016.