The first two ODIs, to be played Oct 15 and 17, will be at the Sinhalese Sports Club (SSC). The third and final ODI of the tour will be played at the Nondescripts Cricket Ground Oct 21.
South Africa lead Sri Lanka 7-3 in 11 meetings to date, with one match in Potchefstroom being a wash-out.
"It's a great opportunity for women cricketers to play regular ODIs, with each match counting towards the the 2017 World Cup," Sri Lanka captain Chamari Athapaththu said, in an ICC statement Tuesday.
South Africa captain Mignon du Preez said series like these will give women's cricket more visibility.
"It provides us players with an opportunity to play a lot more cricket on a regular basis, especially those teams ranked outside the top four. It will surely give women's cricket more visibility," Mignon said.
The Women's Championship is a qualifying tournament for the World Cup with top four sides progressing to the 2017 in England.
The bottom four sides will get a final chance of qualification through the ICC Women's World Cup qualifier in 2017.
With the world's top eight ranked sides participating in the tournament, three series of three ODIs each have been played in the first round, with Australia and the West Indies sweeping aside Pakistan and New Zealand respectively, and England beating India 2-0.