The South African players were also fined 100 per cent of their match fees after the Proteas were found to be six overs short of their target at the end of the one-day match when time allowances were taken into consideration.
De Villiers will miss the ODIs with New Zealand in Kimberley on Tuesday and Potchefstroom on Friday.
The sanction was imposed by David Boon of the Elite Panel of International Cricket Council match referees. De Villiers pleaded guilty to the offence and accepted the punishment, meaning there was no need for a formal hearing.
Cricket South Africa revealed the suspension on its website, stating: "In accordance with Article 2.5.2 and Appendix 2 of the ICC Code of Conduct (the "Code"), which deals with serious over-rate offences, the captain receives two suspension points while the players are fined 10 per cent of their match fees for each of the first two overs short and 20 per cent for every additional over their side fails to bowl in the allotted time.
"Two suspension points in the Code equates to a suspension from one Test or two ODIs, to be applied to the subsequent international matches in which the player sanctioned is most likely to participate in.
"As such, de Villiers has been suspended for the next two ODIs to be played in Kimberley and Potchefstroom on Tuesday 22 January and Friday 25 January, respectively, while his players have been fined 100 per cent of their match fees.
"If de Villiers is found guilty of a second serious over-rate offence in an ODI over the next 12 months, he will receive a sanction of between two and eight suspension points as per the provisions of the Code."
- Sports & Recreation