The Brazilian defender played a key role in helping Dieter Hecking's men to fifth place in the Bundesliga, starting 33 of Wolfsburg's 34 league matches in an impressive campaign that ended in Europa League qualification.
"Naldo is a true leader who proved how important he is to the team throughout the course of the season," said director of sport Klaus Allofs.
"With his experience and character, he is also a vitally important contact person for the younger players. Following the extension with Ivica Olic, this is the next important personnel decision."
Naldo himself, meanwhile, was delighted to have secured his future at the club.
"I want to continue playing successful football with Wolfsburg," he said. "A lot of faith has been placed in me here and I want to pay that back with good performances.
"I feel right at home in Wolfsburg and my family is happy here. For that reason, I am very happy about the contract extension."