Bravo, who had replaced Darren Sammy as the ODI captain in May 2013, has been left out of the squad for the South Africa one-dayers but is a part of the T20 side. Bravo led West Indies to victory in 12 of their 27 completed ODIs since taking over full-time from Sammy.
According to a WICB release,the recommendation to replace Bravo with Holder had been made by the Clive Lloyd-led selection panel and was approved by the board of directors. Lloyd said Holder's appointment had been made with an eye on the future.
Holder, 23, made his ODI debut against Australia in February 2013 and has played 21 games, taking 29 wickets with his fast bowling at an average of 28.65.
"Jason is one of the good, young players who we believe will form part of the long-term future of West Indies Cricket," Lloyd said. "We expect him to be around for a very long time. He is a young man with a very bright future. We have invested in him. He was part of the High Performance Centre and he also played for the West Indies Under-19 Team and the West Indies A Team.
"He has played ODIs for the West Indies before and has done well. We know he will continue to grow and demonstrate leadership. He has a very good cricketing brain and has the makings of a very good leader.
"The selectors decided that now is the time to make the transition and Jason will have people around him to help and guide him. Some might say it's close to the time of next year's ICC Cricket World Cup in Australia and New Zealand but we know that we have a good one-day team which can do very well."
The decision comes two months after West Indies pulled out of their tour to India with one ODI, one T20 and three Tests pending, due to a protracted disagreement between the players, the board and the players' association over the payment structure specified by the players' revised contracts. Bravo had vocalised the players' stance in several letters to the WICB and WIPA.
Holder said he had looked forward to leading West Indies for a long time.
"I'm very happy to be appointed in this post," he said. "It's something I've always been looking forward to from [the time I was] a youngster. Obviously being able to take over the mantle of Dwayne Bravo is big boots to fill. [I'm] just trying to move the team forward."
West Indies are ranked eighth in the world in ODIs, with only Bangladesh and Zimbabwe behind them. Holder called it a "huge task" to revive the team's fortunes.
"We're down the pecking order in terms of the rankings, so it's about getting the guys together as best as I possibly can and trying to move up the rankings," he said. "I just want to take it step by step.
"First time will be the series against South Africa. I think it's key that we build some momentum going into the World Cup but I don't really want to look too far down the road, to be honest, I just want to take it step by step. My biggest task at the moment is to build trust, build relationships with players and try to get the best out of them in key situations in games."
Holder will be captaining a number of senior players and former captains, but said the task didn't faze him.
"I obviously look up to all the senior players in the squad," he said. "My role has primarily just shifted a little bit into leading and guiding these guys. It's something I'm up for.
"I think I'll have the support of the senior guys because I have a pretty good relationship with them. It's just about moving West Indies cricket forward and I think most of the guys can buy into what I'm going to put forward, and I think that is best for West Indies cricket."