Fontaine had a spell on loan with the Glovers from Fulham in 2004 and played under Johnson at Bristol City in 2006.
He has proved to be a rock at the heart of City's defence since that move, making nearly 250 appearances, and Johnson is delighted they are being reunited again.
Johnson said: "I am very pleased to have the opportunity to bring Liam back to Yeovil. I know him very well and have spent many seasons working with him in the past.
"He has great experience in the Championship and we know exactly what we are getting from him.
"He has worked and played with both Terry Skiverton and Darren Way. Liam is someone who we won't have to spend time with to get into the Yeovil Town mentality."