De Villiers was suspended for the opening match of the series as punishment for maintaining a slow over rate during the World Cup semi-final against New Zealand in March.
"AB's presence and contributions will be missed, but we have a hectic playing schedule this season and we felt this would be a great opportunity to develop the next tier of batters during this series, like we are doing with our bowlers," coach Russell Domingo said in a press release from Cricket South Africa on Tuesday.
"We would also like to give him the peace of mind of being close to his wife with the imminent birth of his first child."
Test skipper Hashim Amla, who is vice-captain in the 50-over format, will lead the side.
Domingo also confirmed leg spinner Eddie Leie will remain in Bangladesh for the ODI series having helped the Proteas win the two-match Twenty20 series 2-0.
Image: AB de Villiers
Photograph: Phil Walter/Getty Images