His previous deal was due to expire next summer and his new one now includes an option for a further year.
The club's director of football, Daniele Prade, said that he was delighted that Viola's "fantastic captain" was staying.
"Manuel is very important for us, we are all very proud of him," Prade told a press conference.
"Manuel is the prototype of player that anyone would want. He is educated, clean-cut and above all, he is a fantastic captain."
The left-back has made 239 league appearances since joining the club in 2005.