Boucher will lead a 14-man squad for the August 14-29 event, replacing Ashwell Prince who is captain for the ongoing Test series against Sri Lanka in place of the injured Graeme Smith.
Left-handed Prince, the first black cricketer to lead South Africa, remains part of the one-day squad, convenor of selectors Haroon Lorgat said on Monday.
"With Ashwell not a certainty in our one-day side, we have asked Boucher to captain the team," Lorgat said in a statement issued by Cricket South Africa.
"With injuries to some key players, we have an opportunity to look at others as we build towards the World Cup in the West Indies next March."
South Africa will be without four one-day regulars: Smith, all-rounder Jacques Kallis, batsman Justin Kemp and seamer Charl Langeveldt.
South Africa play Sri Lanka in the opening match at the Premadasa stadium on August 14. Each team plays the other twice in the league, with the top two advancing to the final.
South Africa's one-day squad:
Mark Boucher (capt), Boeta Dippenaar, Loots Bosman, Herschelle Gibbs, A.B. de Villiers, Shaun Pollock, Johan van der Wath, Robin Petersen, Andrew Hall, Andre Nel, Makhaya Ntini, Ashwell Prince, Roger Telemachus, Thandi Tshabalala.
Coach: Mickey Arthur.