The date of Van Niekerk's arrival will be determined after the announcement of South Africa's World Cup squad on July 23.
Van Niekerk said: "It's an absolute challenge to come overseas and to come to a club that's as rich in tradition and history as Northampton is an awesome thing.
"I could not believe the supporters when I came to watch the game, they were very passionate. I'm looking forward to it immensely."
Northampton were relegated from the Premiership last season but have already signed Scotland prop Euan Murray and Wigan full-back Chris Ashton for the next campaign.
Saints director of rugby Jim Mallinder said: "Joe will be a key part of the squad over the next few years and brings undoubted experience and leadership.
"Joe's contract is a big commitment, not only by him but for the club.
"In signing him for three years we are taking a longer-term view on the contribution he will bring to Franklin's Gardens and are delighted that he will be joining us."