De Villiers has asked Cricket South Africa to relieve him of his duties as Proteas ODI captain.
In a statement released on de Villiers' behalf by Cricket South Africa, the cricketer denied accusations that he was being selective about matches.
He assured full support to Faf du Plessis, who has largely been acting as captain of the side in his absence.
"A lot has been said and written over the past 12 months, and I feel it is time to make my position absolutely clear," de Villiers said.
"Together with CSA, we have tried to develop a viable schedule which allows me to prolong my career for as long as possible."
The 33-year-old's recent slump in form prompted speculation that he might retire from one format of the game with the 2019 ICC World Cup in focus.
"...This strategy has prompted some people to say I am picking and choosing when to play for the Proteas, and even to suggest I am somehow putting myself before the team. That is simply not true. That has never been true."
"Faf du Plessis has proved to be an outstanding captain of the T20 and Test teams, and bearing this in mind, I have informed Cricket South Africa that I would like to step down as captain of the ODI team.
"It has been an honour to lead the team for the past six years, but it is now time for someone else to take the ODI side forward.
"Whoever is chosen as the new ODI captain will have my complete support."
De Villiers said he was feeling "refreshed and revived" after his recent break, but wanted to get back onto the field from October onwards.
"That was my promise when I made my debut in 2004; and that is my promise today," he added.
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