The link was set up in February to help the foundation deliver the former South Africa president's messages of education and social inclusion.
But Sunderland sparked controversy by taking on Italian Di Canio, who has previously identified himself as "a fascist" and refused to answer questions on the topic when presented to the media on Tuesday.
The not-for-profit foundation, though, revealed it had decided to pursue its partnership with Sunderland, following a meeting with Di Canio and club officials.
"The Nelson Mandela Centre of Memory and the management of Sunderland Football Club met in England on Monday, 1 April 2013 to discuss the public debates around Sunderland's new coach. Mr Di Canio participated in the meeting," the foundation said in a statement.
"The Centre recently entered into a partnership with the club designed to promote the legacy of our Founder, Nelson Mandela, and to help ensure the future sustainability of the Centre.
"At the heart of the partnership is a commitment to our Founder's values with a special focus on human rights and anti-racism. At the meeting on Monday, Sunderland reaffirmed its commitment to these values and the ethos of the partnership.
"It must be stressed that the Centre's relationship is with the club, not with any individual in the club."
Sunderland's shirt sponsor, not-for-profit business initiative Invest in Africa, refused to be drawn on Di Canio's arrival.
"It is a football-related matter and under the remit of the club," a spokesperson said.