Both players tested positive for the banned stimulant methylhexaneamine following their 23-21 triumph over Ireland last month. B samples later confirmed the results.
Neither player will contest the testing procedures and an investigation and hearing will be conducted in South Africa in the New Year.
"The players returned an adverse analytical finding for a prohibited stimulant, methylhexaneamine, following the match between South Africa and Ireland in Dublin on 6 November 2011," read the SARU statement.
"Both players asked for their 'B' sample to be tested, which confirmed the findings of the 'A' sample.
"The players will not contest the testing procedures or related matters under the 2010 Autumn Internationals Anti-Doping Programme and therefore the investigation and hearing will be conducted in South Africa.
"Investigations remain ongoing and a date for the hearing, as well as the composition of the tribunal, will be announced once those have been completed in the new year."
Ralepelle made his debut for South Africa against New Zealand in 2006 and played against the Lions during the 2009 tour, while Basson made his Springboks debut against Wales in June.